Elite 2: Frontier or Frontier: First Encounters (Elite 3)! Dangerous is good, but nothing surpasses these. Also, there's a political strategy game from 2004 called President Forever that would be a perfect fit for iOS. The fact that it's not here for the 2012 election cycle is a missed opportunity for sure. DEFCON would also be sweet. VGA Trek! A competent Duke 3D port! Project Zomboid!
Seiken Densetsu 3 Front Mission 2/3 Patapon 1/2/3 Monster Hunter Unite Klonoa Star Wars: KOTOR 1/2 all Contra titles Destrega Final Fantasy 4/5/6/7/8/9 Vagrant Story Valkyrie Profile 1/2 Suikoden 1/2/3 I would love these titles ported to the iOS.
For ages I've said Introversions "Uplink", way before it was released the other month on OSX - awesome game.
Super Street Fighter 4 Mario Kart (the Wii version) SEGA Daytona USA One Piece Jump Ultimate Stars Burnout 3 (but hopefully Asphalt 7 will quench my first) New Super Mario Bros
Pathway to Glory or Warhammer 40k squad command. Both by RedLynx and both very good squad tactics games.
There's actually a bunch of Adult Swim games I'm surprised haven't made the jump over: of that batch, the ones I'd most like to see (and think would translate best to a touchscreen platform) would be Titan Lunch Retaliation and Mountain Maniac. I'd play the hell out of both of those.
Pretty much this...any of the PS1-era RPG's would be great. I'm actually quite surprised Squeenix hasn't done this already.
I really have an inkling for Descent 1,2,3 and a game I had on N64 called Forsaken. It was an Acclaim game and it didn't fare too well but I thought the sense of speed and multiplayer were great.
Games like Wild Arms or the good old Terranigma But then my Wife need a iPad herself because i will use mine every second