Most of my favourite games could use a few technical touch-ups. Doom source mods are a good example. Doom at high res with mouse aiming = perfection.
Eternal Darkness could have been less obvious with implementation of the sanity meter. The sanity effects are awesome but if you're totally aware of the sanity meter the whole time then it's not nearly as effective as it could have been.
Hitman Series - Imagine you could rewind back 30 seconds or so anytime throughout your missions... No more starting levels over for minor fuck-ups. Also imagine the game recorded your mission (minus any rewinds), so that you could sit back put your feet up and watch your best playthroughs.
Indigo Prophecy - I love this game and would change much of the story, but it simply fell too far into the realm of stupidity to be redeemable. Heavy Rain sounds like it could fulfill the expectations I had going into IP.