Most characters in the Kane and Lynch games. Lynch is an interesting example in that he seems to prefer being called by his last name by everyone, all the time, even by his girlfriend in the second game.
Likewise, the main character of Freelancer, Edison Trent, insists that people call him Trent. His final line of the game is actually "Please. Call me Trent."
Kyo Kusanagi never refers to Iori as anything other than "Yagami." While rules regarding names are different for Japan, his lack of honorifics indicates that he doesn't hold him in too high of a regard. This is also done to show that the rivalry is an impersonal one from Kyo's side, as Iori addresses Kyo by his first name.
Chizuru calls Kyo and Iori by their last names, though in her case she most likely just addresses the Japanese social rules as well as their heritages (rather than them as persons) and tries not to antagonize either of them directly.
Several people refer to either Iori or Kyo by their last name. I.e., Shingo calls Kyo "Kusanagi-san" to show his extreme respect for him.
Kyo's girlfriend Yuki tends to go by the First Name Basis + "-san" formula with everyone (including Iori), however she refers to Shingo as "Yabuki-kun" instead.
In the case of the Sakazakis, only Takuma is referred to by his last name. Presumably this is because he's the patriarch of the family and for practical reasons.
Phoenix Wright and Miles Edgeworth always refer to each other by their surnames. The only ones to refer to Edgeworth simply as Miles are Redd White, a pompous idiot, and Marvin Grossberg, who presumably knew him from childhood through his father. For the rest it's 'Edgeworth' to Phoenix, 'Miles Edgeworth' to Franziska and 'Mr. Edgeworth' to everyone else apart from Wendy Oldbag, Larry Butz, and Damon Gant, who use nicknames for him. Even Manfred von Karma refers to him as "Edgeworth" rather than Miles.
Franziska seems to switch between his full name and Miles during Investigations depending on her intent. She is also an example of this trope herself as she is refereed to as von Karma (Even in her name box) by Phoenix and Ms. von Karma by everyone else except Edgeworth and her Father. Her text box name even appears as Franziska in Investigations rather than von Karma like it has in past games.
It's notable that Phoenix drops the Last Name Basis with Edgeworth at exactly one instance, where he remembers their childhood and refers to him as 'Miles'. It returns quickly after this, however, and permanently sticks, even after they restore their old friendship. This was probably done in order to show that, despite being friends again, there relationship is still not the same anymore that it used to be prior to the DL-6 incident.
During the course of Geist, no one ever refers to John Raimi by his first name. Then again, if you had his name, wouldn't you want everyone to call you by it, too?
In Mass Effect, the main character is always called "Shepard," even by someone you just had sex with. This is because you can choose your character's first name, but the game is fully-voiced. Urdnot Wrex, meanwhile, is not an example, even though everyone calls him "Wrex"; krogan names give the clan name first, in the same fashion as real-world Japanese names.
After two games of playing it straight, Mass Effect 3 hangs a lantern on it when Dr Chakwas and Shepard sit down to drink together. Chakwas notes that Shepard has never called her by her first name. "Well, neither have you." Chakwas replies that she never will, as using Shepard's first name would be a disservice to everyone she's fighting for.
"That...makes no sense."
"Consider it a lady's prerogative, then."
Some of the party members tend to go by Last Name Basis; Ashley is almost always addressed as "Chief Williams" or "Williams" through most of the first game, and this also applies to Kaidan to a lesser extent. James Vega in the third game is most often called by his last name by his fellow crew members.
Similar to the Mass Effect example, in Dragon Age II, everyone calls the main character by their family name, Hawke, for the same reason— the game is fully voiced. The game dialogue tries to avoid the awkwardness of having Hawke's family or long-term, live-in love interest call them by their surname, but it still happens from time to time. However, in salutations of letters from family members, Hawke will be referred to by his or her given name.
It's also a little weird when you have your sibling in your party and NPCs still say things like "So, you're Hawke." Your sibling never mentions that he/she is also a Hawke. Of course, in many cultures, the eldest son and head of the household is referred to by their family name, so this makes some sense.
Played with in the Legacy DLC. Hawke and their sibling get attacked by the Coterie, since they were tasked with finding the blood of "The Hawke"... and they were a little unsure which Hawke was actually required?! Taken further when you later discover that your father Malcolm was also referred to as "The Hawke", which leads to some conversations, where all three are referred to by this title, completely interchangeably.
This trope is averted by Oriana, your elven maid. As a former slave, she's been instilled with the unconscious urge to refer to someone in authority as "Master/Mistress". This is despite Hawke insistance that she's not a slave anymore and is free to refer to them by their actual name.
Applied to Mahariel, the Warden from the Dalish Elf origin, whose clan appears in II's subplots. Everyone calls them by their last name, including childhood friend Merrill. It's still a step up from just "Warden" or "Hero of Ferelden".
Ijuuin Enzan of Rockman.EXE is called by his given name. However, his counterpart Eugene Chaud's given name comes up precious few times over the course of six games, and only when he is introducing himself by his full name. In fact, it's so unknown that Chaud's NT Warrior version was dubbed into "Chaud Blaze". The dubbers apparently couldn't be bothered to find out that Chaud wasn't his first name. (It was also mispronounced as "Chodd".)
Cidolfas Orlandu/Orlandeau (differing translations) of Final Fantasy Tactics is generally known by either his last name or as T.G. Cid (short for Thunder God Cid). The game system itself refers to him by his last name, though every other character is referred to by their first name.
Aldebert Steiner of Final Fantasy IX is almost always referred to as Steiner, or occasionally "Rusty" by Zidane. He also holds the privilege of being the only Final Fantasy character to have his surname determined by the player.
Final Fantasy VII: Averted. While many characters have first and last names, it seems to be common that most people get addressed (even by complete strangers) by their first name, regardless of their social or professional status (e.g., Rufus, Lazard, Reeve). Therefore, when only one name for a character is known (e.g., Hojo, Kunsel, Reno, etc.), it's impossible to know for certain whether this is their first or last name.
Not exactly a true full name, but it still counts: Solid Snake from the Metal Gear series is usually addressed as "Snake" and never as "Solid", even when he is mentioned alongside his clone brothers, "Solidus" and "Liquid", who share the "Snake" codename. "Big Shell Evil", one of the "Snake Tales" in Metal Gear Solid 2: Substance even lampshades this.
Also happens to Solid Snake's predecessor, "Naked Snake", but in his case its justified since he's the original "Snake" and calling a man "Naked" doesn't exactly sound right. This switches to Full-Name Basis when people start calling him "Big Boss".
Of course none of these are their real names, only code names.
Sam Fisher of Splinter Cell is almost always referred to by his last name, especially by his Voice with an Internet Connection, Lambert. That's Irving Lambert. And then there's Grimsdottir. Pretty much everyone is called by their last name in this series.
Sam always calls her "Grim" for simplicity's sake.
All the Chosen in Eternal Darkness are referred to by their first names by the in-game text except for Edwin Lindsey, which could be chalked up to One Steve Limit, seeing as there's also an Edward.
Paul is consistently "Brother Luther" to the people he interacts with in his time period. Michael Edwards is "Edwards" to his superiors, and refers to two dead firefighters by what may be their last names. Last Name Basis seems most common in the actual dialogue, when the characters have last names.
There is only one person in the entire Resident Evil franchise who refers to Albert Wesker by his first namenote Excella Gione, RE5. To everyone else, he's simply "Wesker."
In Racing Lagoon, Last Name Basis is very common with an except for The Chick (yet the main character calls her by last name) since the game takes place in the year 1999 of urban Japan. While you can name your main character's first name, it's more or less being referred to by another character in the entire game.
In Persona 3, Mitsuru Kirijo refers to most of the SEES team by their last names. The only exception in the beginning is Akihiko, a fellow senior which whom she has quite the history. She'll call the male protagonist by his given name if he romances her, and she starts calling Yukari Takeba by her first name as well (like in The Answer), after some quality bonding.
And in Shin Megami Tensei: Strange Journey, the protagonist is more commonly called by his last name (as opposed to first like in other SMT games), even in menus and the battle screens.
Nobody is sure what Lady Vashj's first name is. Everybody (apparently, even her mother) referred to her as "Lady Vashj".
Use of last names seems fairly common in Gilneas. King Genn Greymane is typically called "King Greymane" by everyone except his wife and his old friend Darius Crowley.
Grom and Garrosh Hellscream are often referred to by their last names, and Garrosh tends to use his last name when assigning things as his, such as in his Catch Phrase, "Hellscream's eyes are always upon you."
"Hellscream" is less of a last name and more of a nickname thanks to Grommash's (Grom's full name) very loud voice. It's mentioned in the novels that nicknames pass from father to son after the former's death. Orgrim wasn't called "Doomhammer" until his father fell in battle and passed on his warhammer to his son. Thus, Garrosh didn't become Hellscream until Grom died fighting Mannoroth.
Both played straight and averted in the Gears of War game series. Averted with the two main characters, Marcus Fenix and Dominic "Dom" Santiago, who are almost exclusively called by their first names. Played straight with Damon Baird and Augustus "The Cole Train" Cole, who are almost exclusively called by the last names, or in Cole's case, his Thrashball nickname.
Rose of Sharon Cassidy is also on a Last Name Basis with everyone as well, being called Cass. She herself mentions she's not a huge fan of her first name after it evolved into an Embarrassing Nickname, Whiskey Rose, for her heavy drinking habits and rosy cheeks. Now the only people who call her Rose are those who quickly find themselves lying on the floor of a bar.
Inazuma Eleven: In Japan, unless you're a girl or the heroes' relatives, expected yourself to be called by your last name. Even the protagonists are not immune to this.
However, Tenma, the protagonist of the sequel GO, and his best friend Shinsuke are more often than not referred to by their first names. This trope is still in full effect for everyone else.
Masami von Weizegger, hero of Ring Of Red, identifies more with his German heritage than with his Japanese heritage, so he insists that others call him "Weizegger" instead of "Masami".
Very common in the Call of Duty series. In the World War II-based games, only Russian protagonists are even given first names. Later games do give all player characters full names, but everybody still primarily calls them by their last name. Commanding officers fare little better.
The Tokimeki Memorial series, starting from Tokimeki Memorial 2, allows the player to choose how they refer to characters as part of gameplay - moving to First Name Basis too early (or choosing an insulting name like 'Bookworm') will cause a drop in affection and the character to ask not to be called that way. Some characters, out of politeness, will always or almost always refer to the player character by their last name, such as Hikami from Girl's Side Second Season, who will always call the protagonist '<last name>-kun'.
At the beginning of Little Busters!, Riki is on a Last Name Basis with Komari, Haruka, and Kurugaya. He starts calling Komari by her first name after she does so for him after she joins the baseball team and Haruka explicitly asks him to use her first name part-way through, but Kurugaya, who cultivates an image of a beautiful, competentCool Big Sis, is very insistent that everyone call her 'Kurugaya' or 'Anego' - anything but by her cute first name 'Yuiko'.
In Red Faction, Parker is only ever addressed by his last name. It would be harder if he had a first name to begin with.