Some of the Robot Masters have Alliterative Names just by virtue of their gimmick starting with M, e.g. Magnet Man, and the title character.
X series: In Mega Man X: Armored Armadillo. In X2: Overdrive Ostrich and Morph Moth. In X3: Blizzard Buffalo and Crush Crawfish. In X5 (none in X4): Dark Dizzy. In X6: Shield Sheldon. In X7: Soldier Stonekong and Tornado Tonion. X8 has Vile V.
From Mega Man Star Force you have Sonia Strumm and Bud Bison. There's also the Wave Changed form of Damian Wolfe, Wolf Woods.
Battlefield Heroes loves this: Buccaneer Bay, Coastal Clash, Seaside Skirmish, Victory Village... and that's just (ALL of) the levels! Burning Bullets, Troop Trap, and almost all of the weapon names: Greg's Greasy Gun, Wolfgang's Wonderful, Florenz's Flurry, etc.
In Donkey Kong Country 1 to 3, in addition to levels, the worlds nearly all have alliterative names, with names like Monkey Mines, Vine Valley and Gorilla Glacier, while the second has Gangplank Galleon, Crocodile Cauldron and Krazy Kremland.
Every level in Donkey Kong 64. Jungle Japes, Angry Aztec, Frantic Factory, Gloomy Galleon, Fungi Forest, Crystal Caves, Creepy Castle, Hideout Helm. Even the majority of the minigames have alliterate titles. Also arenas, one of the shooters, and most of the Cranky abilities (a couple of the exceptions go with rhyming instead).
Donkey Kong Country Returns continues the alliterative level names with stuff like Poppin' Planks, Rickety Rails, Muncher Marathon and Furious Fire.
It extends to the names of certain characters as well: Cranky Kong, Candy Kong, and King K. Rool.
Gailardia Galan Gardios from Tales of the Abyss. You probably know him better as Guy, though.
Not characters per se, but a number of the starting scenarios in the X-Universe games have these. Some examples are "Tormented Teladi," "Boring Boron," and "Lost Lar."
The Jump Start edutainment games series introduced 4 characters in JumpStart Preschool to which this trope applies: Casey Cat, Eleanor Elephant, Kisha Koala, and Pierre Polar Bear. Too bad Kisha was retconned into a tiger in 2005, ruining the Added Alliterative Appeal! (Pierre also got turned into a different species, but the alliteration was maintained - he became a panda.)
Toontown Online has lots of denizens that have alliterative names such as Clerk Clara, Fisherman Furball, Tim Tailgater, Nina Nitelight, and Fast Freddie. Incidentally, Fast Freddie's building takes this to the extreme: Fast Freddy's Fretless Fingerboards (Fabricated From Figured Fir!).
In addition to the series and game titles, most of Rage Racers in-game music tracks are alliteratively named ("Silver Stream", "Mech Monster", "Volcano Vehicle", etc.), with the exception of "Mathemabeat", "Industria" and "Stimulation".