I got 100% kills on every level and every route in Panzer Dragoon Zwei. I also played NiGHTS into dreams every day for six months straight. Yeah, those two games I knew by heart :).

Ratchet and Clank 2 and 3, I replayed those games alot. Seriously once when I was at a sleepover at my friend as a child we finished ratchet and clank 2 five times in 24 hours.

I've played lots of games but I don't understand the question really. I mean sure I can speed run Crash pretty well, or have little effort on Very Hard difficulty in Tekken but I don't think I've truely mastered any game.

However, Time Crisis. I got this on PS1 and played it enough that I knew where every enemy popped out. So when I went into the arcades I could complete it on 1 credit.

That's the only ratchet and clank game in the series which I have not finished. I'm still halfway in it, good game so far.

Have you played Into the nexus?

As of now no. I will try to buy it soon though. Is it good?

I liked it alot (But I'm a huge R&C fan though ). The biggest downside is that its kinda short, but with challenge mode you still get a good amount of content.

Damn I loved that game, it and Unreal Tournament was basically my gaming all through high school. Was nothing quite like rail gunning someone whilst mid-air across the map when they're only 1-2 pixels in size (800x600 res, 14" monitor ftw). 

Metroid: Prime

Replayed it ~10 times. Not a full-on master, but I can breeze through it easy enough.

Megaman games. You pretty much master them to get through, and if you keep your skills up to date and remember a few patterns you can complete the entire game way faster on any subsequent play through.