I also have a lot, but... somewhat less overlap than the average Neospring user. Since I rarely finish games, I basically consider any game I'm able to finish to be a favorite, with bonus points if I keep returning to it.

Doom (1993) + Doom II, Morrowind, WarioWare: Mega Microgame$, the first three Rhythm Heaven games, The Stanley Parable: Ultra Deluxe, SuperTuxKart, the entire Ace Attorney series, Minecraft, and various arcade games such as Dig-Dug and Tetris.