I only spent a little time with a pal's copy of Ninja Gaiden. I liked what I saw, but I can't include it. Likewise with Metroid Prime 2, which I haven't picked up at all.
All that being said....
1 - Splinter Cel: Pandora Tomorrow (Just a fantastic game on so many different levels)
2 - Halo 2 (Nice progression from the first game and although a bit short still pretty solid)
3 - Kotor 2: The Sith Lords (Not as good as the first and lots of unfinished stuff, but overall a pretty good play)
4 - Paper Mario 2 (cutesy, but a fine way to kill some time
)
I should be getting my hands on Ratchet and Clank 3 over the holidays. I mention this because I had such a good time with 1 & 2. I expect Up your arsenal to be just as good as the first two and based on that assumption, it would probably make my list.