Out of all the many millions of game franchises in the world, very few have had a NeoGeo conversion. The ones that come to come to mind immediately are Strikers 1945+, PuzzleBobble and NeoBomberman. I suppose the fact that the Neo is primarily an arcade machine doesn't help for conversions of games that really are 'console' games. And also the fact that sales wouldn't have exactly been huge at $250+ for an AES version.
So, what games from the 16/32-bit eras would you liked to have seen NeoGeo versions of, irrespective of whether the game would have worked as coin-feeding arcade games.
Personally, I'd love Neo versions of Castlevania and Contra. Also a NeoDarius with massive pre-rendered fishies would be cool..
And something from Treasure. No idea what, but if only they'd been let loose with a Neo dev kit I'm sure they'd have come up with something amazing.