Capcom's got a nice few here and there:
Bionic Commando got a GBC game that takes the basic premise of the NES game and then made a GBC exclusive spinoff. If you like classic BC gameplay, its worth tracking down.
Ultimate Ghosts n Goblins was a long time coming sequel to the GnG series that'd be mainly dormant for many a year. But its a fairly well known game comparatively speaking - so what about Ultimate GnG Kai that was released in Asia? Its the same basic game as Ultimate GnG but it its main mode tweaks the game design so that you are back to having fixed check points, and only two hits worth of damage before you die - the upshot is that there are less enemies in levels, and enemy spawning is drastically reduced to compensate. The shitty ring fetch quest for the best ending is axed, in their place is a slightly harder second run through of the game (with the witch boss fight placed between the first and second runs). So basically - it refines and improves upon the original Ultimate GnG giving me a much more fun and balanced game. And as a bonus, the original version of the game is available in Kai as well, if you'd rather play that version.
Sticking with GnG, did you know it got a Wonderswan version/sequel? Its a pretty decent game as well, all things considered. I've not finished it yet, but if you want more GnG, its well worth tracking down.
And sticking with the Wonderswan - Mega Man got two of them - Rockman and Forte (which despite its name, IS NOT a port of the Super Famicom game but rather an all new sequel) and Rockman.exe
RM&F is pretty garbage though. Its got all new bosses and levels (fear the mighty Compass Man!) and honestly, its hard to say anything positive about it. It looks bad, sounds bad, plays bad.
Rockman.exe though is way better. Its not an RPG but a platformer like Network Transmission on the Gamecube. It sorta takes inspiration from the first two EXE games - each main level of the game will have a point where the path diverges - one path goes up, the other down. Depending which path you take, takes you to a completely different area and is themed around a specific navi. At the end of each path you get a unique boss fight against a net navi. Clear the game by beating Life Virus and you can then replay the game and if you take alternate routes on each level (basically - make sure you beat each unique navi) you'll get a real final boss after the Life Virus - Gospel. And then if you can clear the hardest survival/boss rush mode you can fight Forte. Only thing that lets it down a bit is the controls and sound. But well worth a look.
Stepping away from Capcom, and over to my other favourite series - Yakuza, I'd be silly to not mention that the PSP got two brilliant Yakuza spinoffs that remain exclusive to the system to this day:
Kurohyou 1&2 are games that follow the delinquent Tatsuya as he gets caught up in a war between the Tojo Clan, shady government conspiracies, and even an east vs west fight between Kanto and Kansai fighters.
Content wise, its Yakuza - Kamurocho is in both games, Sotenbori returns for the sequel, tons of mini games that you have come to expect from the series as well as new gambling games, part time jobs (dream no more of being a bouncer for Club Shine or working at Smile Burger!), combat wise its done by the same team that handled Def Jam Vendetta/Fight For New York (and it translates to Yakuza incredibly well), excellent soundtracks, and interesting plots that use a cool animated comic book style as opposed to full blown FMV cutscenes.
Its really impressive just how much is crammed onto the system - especially the sequel. And fights run in 60FPS! If you want Yakuza on the go, these are the best choices available!
Same goes for the GB version of Bionic Commando with it's anime sci-fi art instead.
Its a really overlooked gem, in my opinion - I was expecting it to basically be a GB port of the NES game but to my surprise it was its own thing - clearly taking the NES game as inspiration but not outright copying it level for level. I still remember how badly the last level kicked my ass - that bit where your grappling from rocket booster to rocket booster, with a bottomless pit under you... took me many a try to clear!
