"...I'm no engineer and correct me if I'm mistaken, but don't you have rather a design flaw in these things? Now, don't get me wrong: God created a lot of useless, stupid-looking things on this world too, but he didn't see fit to make any of them three-legged. Why was that, do you think?"
The Gundam SEED spinoff manga Delta Astray has the Guardshell, which can change from a tripod to a Gundam-like form that uses the tripod's carapace as a giant yo-yo. Considering it was designed and piloted by a Martian, it's definitely a Shout-Out to War of the Worlds.
Deconstructed in Slipping Between Worlds. A group of "visitors" from Roundworld (Earth) provoke a mass panic that Ankh-Morpork is being invaded by pitiless alien conquerors. The possibility of a Slight Disagreement Of The Worlds is explored in Discworld style, and includes stolid Discworlders debating the self-evident drawbacks of top-heavy tripod war machines. A farmer looks down at a cattle grid and nods, saying "I'd like to see 'un get over this 'un!", while a Man In A Pub smugly discusses how unbalanced a tripod would be to, for e.g., a troll or a golem grabbing one leg and flipping it over. "Sides, your golem. Made out of invulnerable heat-resistant ceramic. Your troll. Fire a death ray at him, just makes him dumber and angrier. Them tripods is just scrap metal either way!"
Even the 1950s "floating" War of the Worlds Martian war machines have, if you look closely, 3 repulsors keeping it hovering in the air. (They originally planned to have the usual tripods, but the amount of money available and the limited technology of the day led them to change it to more fit a "Flying Saucer" motif)
In War Of The Servers, the Mingepods aren't even really tripods. They have two front wheels, and a third "leg" with another two wheels on it. So while they're technically tripods (three 'legs') they still have four points of contact.
Lightning McQueen has a dream where he stars in a movie about spark plug tripods (actually "quads," as they have four legs) destroying the city in Cars.
Scary Movie 4 attempts to spoof The War of the Worlds with the triPods, which resemble an iPod on three legs with a "Destroy Humanity" playlist.
Even Star Wars is not exempt from this. Though not as huge as most other examples, the Droidekas are functionally tripods when they're not rolling around as wheels. They aren't meant to move around much like this, though; it's mostly just to steady them, like an actual tripod.
The Walkers in the original trilogy were inspired by the War of the Worlds tripods.
Aside from being four-legged, the spider droid matches the Wellsian Martian fighting machine, right down to the heat ray. Only the traditional black-smoke bomb launcher (which rarely appears outside Wells' literary masterpiece) was replaced by an anti-personnel blaster cannon.
R2-D2 himself is tripedal, although his supporting struts don't bend and he rolls rather than walks.
The Lost in Space movie features a race of insectoid creatures with this flaw. The DVD commentary acknowledges this, admitting that nature would never design anything like this because of the off-balance problem.
Arthur C. Clarke's Rendezvous with Rama features 3-legged biots used as a sort of mobile sensor. These move very fast by pivoting around on one leg, using each of them in alternation, and reversing the direction of rotation from time to time. As a matter of fact, a 3-part symmetry is central to all things Raman.
Larry Niven's Rainbow Mars features creatures with these — they are meant to be roughly the WOTW Martians, had they lived on the same Planet Mars as the Barsoomian Martians, the "Martian Odyssey" martians, the "Out of the Silent Planet" martians and the Flash Gordon Martians. Niven calls them the Softfingers or Astronomers, depending on who is talking about them.
The series Warstrider features an inversion, as the tripods are actually the humans' titular mecha.
The Day of the Triffids goes into a bit of detail about how the titular walking plants move, comparing them to a man on crutches and specifically noting that it's not an especially fast or stable method of locomotion. Being plants, of course, they don't really need to move very often or over a great distance.
Wayne Barlowe's Expedition has a number of tripodal creatures, such as the Sac Back, Beach Loper, and the Groveback mentioned below.
The album cover for Doctor Steel's album, People of Earth, shows an attack by giant tripod robots reminiscent of The War of the Worlds - only in the foreground it shows Dr. Steel controlling them. (A similar tripod is seen in the background of the album art for The Dr. Steel Read-A-Long.)
Classic BattleTech doesn't yet because the timeline hasn't yet advanced that far. It's only a matter of time, though, since Catalyst Game Labs are dedicated to considering the Dark Age effectively Canon Yet To Come.
In Monsterpocalypse, the Martian Menace faction has some figures based on the tripods from War of the Worlds: the monsters Deimos-9 and Phobos-7, and the Reaper and Despoiler units.
Dungeons & Dragons has several three-legged monsters, such as the Xorn, the Otyugh, and the Triapheg.
The Combine Striders and Hunters of Half-Life 2 and its episodes.
Scrin Annihilator and Reaper Tripods from Command & Conquer 3. The aliens just love these things.
Red Alert 3 has the Shogun Executioner in two scripted missions, a Humongous Mecha with three legs and three torsos, with each torso shaped like a samurai complete with a Laser Blade. The thing is so big it can destroy aircraft just by walking at them. It's especially effective against the Soviets, as electrical attacks only serve to heal it.
Tripods also appear in Pikmin, but the ships never use their legs to walk.
Colossi in StarCraft II may have four legs, but they are otherwise totally in fitting with the spirit of the trope. They fry stuff at extreme long range with sweeping heat rays, and have very long stilt-legs that let them stride over any terrain with ease.
... and Defilers, and Detection Drones, and Reaper drones. Honestly, the Hierarchy is this trope.
Darkwalkers and Scavengers from Unreal Tournament III. The Darkwalker is the classical Humongous Mecha variant of this trope, armed with a dual laser cannon. It is one of the stronger vehicles of the game. The Scavenger is a small but fast vehicle that runs on three tentacles. One of its attacks is turning into an electrified ball and roll into enemy players.
Crysis 2 has tripod drones known as Pingers, who substitute the death ray for powerful sonic weaponry.
The boss Tripod Sardine from G-Darius. See Real Life entry below.
A particularly gigantic instance of this trope in the form of the Teraformer in Jak3. The thing is so big, that after you take it down with a vehicle, you have another fight on its wreckage with plenty of room to maneuver around.
Fallout 3 has Sentry Bots, which are one of the game's most fearsome enemies. Also, Mister Handy/Gutsy, which resembles the aforementioned The War of the Worlds tripod bots.
In Quake IV, as a possible shoutout to the aforementioned Droidekas, the Convoy drones roll into battle before deploying tripod legs. Luckily, they don't have deflector shields.
Referenced in The Venture Bros., where Dr Venture transforms HELPER into a classic tripod "walking eye." When asked what they're good for, Venture is at a loss, apparently convinced by popular sci-fi that they're simply a requirement. Random scenes of destruction also occasionally show a tripod terror running amok.