Dio Brando's Stand Za Warudo as well as a number of other character could qualify. Dio's ability to stop time was kept a secret from his enemies, and he used it to perform all sorts of seemingly-impossible stunts. In the anime version, he made it look like things around him were exploding or tearing themselves apart because he willed it. Being able to stop time, if only for a few moments, made him virtually invincible.
In fact, for quite a while the major villains of each arc had powers relating to time. Dio's The World could stop time, Kira's tertiary Another One Bites the Dust can invoke time loops, Diavolo's King Crimson can erase small spaces of time, and Pucci's Made in Heaven could accelerate the flow of time to unbelievable levels. Even Funny Valentine in Steel Ball Run, while not able to affect the flow of time, weaponizes the ability to travel between parallel timelines—arguably mastery over space.
Steel Ball Run did indeed have a straight Time Master adversary in Ringo Roadagain. However, Mandom's temporal recursion ability (reset everything back to the way it was six seconds ago, but with everyone knowing what had happened in that time) doesn't give Ringo that much more of an advantage than anyone else, because (a) he deeply believes in Explaining Your Power to the Enemy (it wouldn't be a fair fight otherwise, and (b) he gets reset along with everyone else. Knowing what's going to happen is his only real advantage, so it's ultimately just an oblique form of precognition. Defeating him proves to just be a case of getting him into a situation where the reset's knowledge won't allow him to escape, because there's no avenue of escape.
This is Subaru's Seishi power in Fushigi Yuugi. Which she uses on her husband Tokaki and herself, reverting them to their younger selves for a while. She also casts a similar spell on her friend Tatara, allowing him to keep his youth as long as he stays in a determined place — which suits him fine because he wants to live as long as possible to protect the Shinzaho.
Ultear Milkovich from Fairy Tail has the ability age or restore inanimate objects. She later reveals that she can travel the entire world back a minute back in time in exchange for making her age to near death.
In Rave Master, Captain Hardner has an interesting way of using time related powers. Namely, restoring old wounds to people, and retgone'ing his own injuries. Sieghart and Niebel, however, as Time Guardians, count as more straight examples. Sieg can make objects and living beings travel through time, while Niebel can manipulate his own time, giving him a massive power boost in exchange for aging in an incredible speed non-stop.
Emiya Kiritsugu from Fate/Zero is a more restrained version of this. He has a magecraft called 'Innate Time Control' which allows him to internally affect time - speed it up for superhuman reaction time in combat, or slow down his bodily functions to avoid a search-and-destroy system. However, whenever he reverts to normal time, his body is forcibly 're-synced' to the time of the World, which can cause very heavy internal injuries.
Ruri from Rising X Rydeen has an ability called "chain of lost memory". This lets her revert anything or anyone back to the it was five minutes ago. So as long as the item or person was injured within five minutes she can fix or heal them.
An example of one such card would be Stitch In Time, from the Ravnica Block.
For a specific character example, the Blue Planeswalker, Teferi, specializes in Time magic.
The Time Wizard from Yu-Gi-Oh!. The anime typically portrays the card effects as the Wizard using its powers to rapidly age monsters to dust, although certain monsters can actually become stronger after a millenium or so.
The D-Heroes also have traces of this as many of their abilities are connected with time (like sending enemy monsters into the future).
Galaxy-Eyes Tachyon Dragon is able to negate card effects and control time to its own advantage during the battle phase. Its Barian-Force upgraded counterpart has an effect that negates the effects of all other cards and resets the entire state of the duel to that of the beginning of the turn and and then averts the occurrence of any unfavorable outcomes during the main phase.
Rip Hunter is The Time Master. He uses his time machine to, in addition to fighting evil and learning martial arts, get the best soda of all time.
The android Hourman, who was built with precognition and chronal manipulation powers on top of possessing a map of all space and time.
Parodied with the D-list supervillain Killing Time in Empowered: he doesn't have any time powers, but really, really wishes he had. So he uses clock-themed gadgets instead - clock hands thrown as darts, a bolo made by joining the chains of two pocket watches, etc. Emp responds with her "mighty power over plant life" — that is, she beats him with a branch until he stops moving.
Same was the case for the DC villain Chronos until he made a deal with Nero, and gained actual time powers
Zero Hour villain Extant had loosely defined time control powers. He killed several members of the Justice Society by accelerating their aging to the point of death, and later he defeated Jay Garrick by regressing him back to an age before he acquired super-speed and became the Flash.
Recent X-Men addition Velocidad was first thought to have Super Speed. This was disproven when Doctor Nemesis had him run across water... and he fell in, unable to move fast enough to not break the surface tension. Turns out he controls time in a localized pocket, giving him the appearance of super-speed outside but still subjected to the normal laws of physics inside.
Likewise, Kiden Nixon of NYX. Time appears to slow down for everyone around her, while still passing normally for her (at one point, she spends months in this accelerated state, while only a few days pass outside it). However, unlike Velocidad, the effect is more than simply Super Speed: She just pokes someone who had been harassing her, and it snaps his arm like a twig.
Yog-Sothoth, from the Cthulhu Mythos, isn't just a master of time - it IS space-time.
In The Alloy of Law, Sliders are mistings who can create a bubble of accelerated time around them, while Pulsers slow down time in their vicinity. Wayne is the former, and Marasi is the latter.
Live Action TV
In Doctor Who, the Time Lords can't do this, at least not without the aid of mechanical devices, with the following exceptions: in Invasion of the Dinosaurs, the Doctor's Time Lord nature provides immunity from time disturbance. In "The End of the World", the Doctor shows that he has a perfect sense of timing, and that he can slow down his perception of time itself.
In the Doctor Who Expanded Universe, trained Time Lords can do this on a small scale, reaching a few seconds across time, usually for combat purposes, and the Celestial Intelligence Agency has operatives who can stop time, or jump a billion years, by willpower alone.
But of course, when they have their technology with them, they will prove exactly why they are called the Time Lords.
Also from Heroes, Peter Petrelli, who copied it from Hiro, and Arthur Petrelli, who stole it from Peter. Besides being Time Masters, all three can also teleport as a result of controlling the space-time continuum.
Dr. Tom, the psychiatrist in Being Erica, seems to have this ability. He not only sends the protagonist Erica back through time but then appears in her history, be it as a hot dog vendor, repairman, street performer, etc. so she can continue to consult with him.
The Kanohi Vahi in BIONICLE gives this power, although with the limitation that only the time around a given target can be sped up or slowed down. It doesn't allow time-travel either. ... Unless you break the thing, in which case it crashes time itself, so that the past, present and future will be all happening at once.
Both Mage: The Ascension and Mage: The Awakening feature the Sphere/Arcanum of Time, which allows perception of the past/future as well as manipulation of the flow of time. Mage: The Ascension has it as a specialty of the Cult of Ecstasy (a Tradition that uses ecstatic measures to enter an altered state of perception), whereas Mage: The Awakening has it as a specialty of the Acanthus Path.
The rare and much maligned True Brujah bloodline from Vampire: The Masquerade can control time with the Temporis Discipline.
Wraiths may gain some control over the passage of time using the Pandemonium Arcanos in Wraith The Oblivion.
Phanes, described in the Epic Level Handbook supplement. They're unwanted children of deities of time/destiny who look like black clouds of various shapes. They can travel back in time, summon a copy of themselves from the future, summon copies of their opponents from an alternate timeline, and freeze themselves or others in time and devour their future (which basically makes their victims grow old at an accelerated rate.)
Warhammer 40,000 introduces the Crypteks of the Chronomancy school in the 5e Necron codex, who use incredibly advanced hyperscience to manipulate time as they see fit. Their aeonstaves can trap victims in bubbles of slow-time, their chronometrons can shift them out of phase with the normal time flow, and their timesplinter cloaks are comprised of protective casings of crystalised time, rendering inert any blow that does not land in the right fraction of a second.
The most adept of all Cryptek Chronomancers is Orikan the Diviner, a Necron Cryptek whose hyper-advanced technology allows him to manipulate the time-stream in very far-reaching ways. He is fully capable of time travel and altering events in the past to suit his plans, and he's one of if not the only individual in the galaxy who is. With such incredible potential at his command, one might imagine Orikan to be a major player in the galaxy's wars, but in fact he is all but harmless. The thing about Orikan is that he, like all Necrons, is a million-year-old robot whose programming has degraded severely. In life he wasn't a technologist at all, but an astrologer and court fortune-teller. Thus the only thing Orikan really cares about now is making sure that his reputation for accurate fortune-telling is maintained, and this he does by going back in time and making sure his petty predictions and prognostications come true. Not the other way round - he doesn't visit the future to see what will happen, or come up with plans first and predict their success later, he just makes whatever he's predicted using traditional astrology happen. That's pretty much the total extent of the use he puts his fantastically awesome powers to.
The titular "achrons" in Achron are Time Masters. Players can pause time, slow it down or speed it up, jump to alternate moments in time and generally observe the entire timeline (timewaves and all). This makes them ideal generals for commanding armies in cross-temporal warfare.
When the Titans shaped World of Warcraft's Azeroth, they chose five breeds of dragon, empowered each of them, and gave them dominion over certain aspects of the world. The Bronze Dragonflight was charged with guarding Azeroth's timeways. Bronze dragonflight questgivers meet your character and get confused about whether they have met you before, they send you to important times in history so you can stop someone else from screwing them up, and their leader is long-missing and is implied to be a bad guy now.
Speaking of which, their leader, Nozdormu, was even granted knowledge of the exact place and time of his own death, so fighting him would be completely stupid. As soon as the fight goes poorly for him, he will just restart the fight from its time of origin and try a different tactic.
The Big Bad of the Freedom Force series is literally named Timemaster. He's essentially a Galactus analog with power over Time instead of Cosmos. He is only incapable of controlling his own aging process, so he plans to gain immortality by literally destroying time itself, with the unfortunate side effect of killing everything in the Universe except him, something which doesn't seem to bother him much.
He also has the problem (for the heroes) that he can, at any given time, revert himself to when he was at his most powerful, making it impossible to defeat him. In the end, only extremely powerful Applied Phlebotinum or the aid of the Anthropomorphic Personification of Chaos is able to make him stay down.
In her "Deflation World" spellcard, Sakuya pulls both the future and past versions of each knife she throws into the present, in effect forming lasers made out of knives.
There is another character with (more subtle) mastery over time: Kaguya Houraisan. Her power control the rate of flow of time, dubbed "power over eternity and temporality" (think Bullet Time). Which saves her from boredom, since she has Immortality. There are WMGs about how she and Sakuya are connected.
On the other hand, the Mysterious Figure from Birth by Sleep demonstrates how a time-wielding boss is done right. One of his tactics involves stopping and rewinding time to recover HP, even reversing the BGM. He has more time-related tricks when he shows up in 3D - in the Japanese version, he even throws out a "TOKI WO TOMARE!".
Viewtiful Joe can speed up or slow down time, though it's explained in-game as 'visual effects', as the game takes place within a movie film.
Flash Man, Bright Man and Time Man from the Mega Man series all have weapons that can either slow or stop time.
This is the only power the protagonist from Braid has, and it gets put to many fascinating uses.
Moebius and his predecessors in Legacy of Kain, the guardians of time, who are among nine sorcerers chosen at birth to guard different aspects of the world.
Time technology shows up a lot in Command & Conquer: Red Alert, with the original breakthroughs made by Einstein. Red Alert 2 introduces the Chrono Legionnaires, who can teleport around and erase other units from history. In the original manual, it's implied that the chronoshift teleportation is actually a case of Time Stands Still while the unit travels across the map the normal way.
Tales of Monkey Island: LeChuck near the end of Chapter 5. When he sees the Vaycaylian warriors throwing their javelins at him at Winslow's order, the villain uses his voodoo power to make Time Stand Still for those outside of LeChuck's ship, making the entirety of the ship seem more like a parody of Year Inside, Hour Outside. Strangely enough, the Crossroads (and Morgan LeFlay for that matter) don't seem to be affected by the voodoo time freeze.
A possible explanation for that is found in Chapter 1; the Voodoo Lady mentions that the Crossroads are the source of all voodoo power (or something like that), and as such are probably immune to voodoo being used as a weapon against them.
Sonic the Hedgehog has this power, but doesn't use it very much (if at all). His rival, Shadow the Hedgehog, uses it much more often, to the point where it can be considered a part of his Elemental Powers. The resident Kid from the Future, Silver the Hedgehog, doesn't have this power naturally, but is only relevant to the plot when he time travels.
Zilean from League of Legends holds the title of Chronokeeper, and he lives up to it. He places time bombs (literal ones) on targets that detonate a while later, can rewind time to reduce his cooldowns, and can speed up or slow down time around champions to increasing the movement speed of his allies or decreasing his enemies'. His ultimate ability puts a protective sigil on an ally that will rewind time around them if they die, essentially resurrecting them if they die while the sigil is active. Early-game, his time bombs make him a great nuker, but as the game goes on, he tends to do better in a support role.
City of Heroes has this as a Buff/Debuff set. It's considered one of the best in terms of performance.
In Space Channel 5 Part 2, the Japanese version mentions that Purge has the ability to bend spacetime.
Chrono Trigger's Big Bad, Lavos, seems to have some influence on time given that his final boss battle takes place against a backdrop that changes to scenes spanning history. His evolution in Chrono Cross.
Dr. Nefarious Tropy, the self-proclaimed "Master of Time" from the Crash Bandicoot series.
In Skyrim, the Dragonborn can learn a Dragon-Shout that literally commands time itself to stop... and it listens.
Tales of Xillia 2 has the aptly named Khronos, who's one of the three prime Spirits who watch over the world and a major antagonist. He initially only uses his time manipulation to speed up his movements, but in later fights, will stop time completely for a brief moment and can even reset the battle to its beginning. The reality-warping abilities of Ludger's Corpse Shell are the only thing that keeps him from being completely unbeatable.
There are two major groups in Homestuck with mastery over time:
Time is one of the powers available to Sburb players, and one of the two which must occur in every session. Dave Strider is the Knight of Time in the human session, and Aradia Megido is the Maid of Time in the troll session. Both are in charge of timeline management - using their powers to establish and take advantage of stable time loops to ensure things proceed as they must, and to provide a way to avertbad futures should things go wrong (which they have... often). Both use music-themed Magic Feathers to travel through time - Dave uses turntables, while Aradia uses music boxes; after ascending to the God Tiers, Aradia is strong enough in her time powers to freeze JackNoir in time without any assistance, however temporarily it may have been. Also, both their Lands house the item necessary to initiate the Scratch, itself a massive burst of time energy.
The Felt each have a different power that allows them to manipulate time or perceive things in the past or future. Well, except for Biscuits, whose "power" is hiding in an oven that he thinks lets him time travel into the future. Technically true, even though he's just traveling at the same rate as everyone else. Actually, his oven doesn't have time powers; it has space powers.
M9 Girls!: Any can generate a bubble inside of which time almost stops completely.
In Red vs. Blue, Gary/Gamma's special AI ability is to manipulate time. The Meta steals it between Blood Gulch Chronicles and Revelation.
Dan from Trinton Chronicles has control over time including accelerating, deaccelerating, and stopping time. As a bonus he gained light and dark generation and control which gives him the bonus abilites to age/de-age (from light) and restore/degrade (from dark) people and objects.
Word of God says there is no time travel in the Whateley Universe, but Stopwatch has the power of temporal warping. He can speed up his own personal time until he's effectively a speedster, or he can slow down someone else's time while he moves at a normal rate.
Virginia from The Platoon Of Power Squadron. At first she can only make time stop, but then she and the gang do a little experimenting and discover she can unfreeze people and create portals to other times and places. There are a few side effects, such as portals to the past being invisible from that end. Naturally, Donald ends up getting lost once.
A somewhat limited example, Clockblocker from Worm can put objects or people in temporal stasis with a single touch.
Dispatch can make a bubble of sped-up time around himself and a few other people. He uses it for combat, as a battlefield medic and as a force-multiplier for heroes whose powers need a ramp-up period.
Cody aka Perdition aka Yangban No. Thirty-Six can for all intents and purposes 'rewind' an object or person back a few seconds in time.
Phir Sē can create portals that deliver their contents forwards or backwards in time which he exploits to create an infinite loop, allowing for an attack with effectively unlimited energy.
The fourth Endbringer, Khonsu, can create inescapable bubbles of sped up time that cause anyone trapped within to starve to death or die of old age.
Parodied on Johnny Bravo with Chronos, Master of All Time! *Dramatic Thunder*: A talking Grizzly bear who had dubbed himself Master of All Time! *Dramatic Thunder* due to having stuffed his cave full of watches that he all meticulously kept precise time on. Well, except the VCR clock. That one was beyond even his vast and immaterial powers.