1. Pokemon Silver (going based on what I enjoyed the most at the time. Obviously Pokemon White is better now.)
2. Fallout 3 (I've logged 500 hours into this, and have played through the entire game 4 times.)
3. Ratchet and Clank: Up Your Arsenal (introduced Dr. Nefarious... nuff' said.)
4. Jak 3 (great music, great settings, great gameplay, great difficulty, and great story... the final game of one of the best trilogies of all time.)
5. the fifth spot is tied between Sly 3: Honor Among Thieves, and Kingdom Hearts 2.... honestly, I liked the gameplay of Sly far more, but the story of KH2 was great as well...
As for the pokemon, well call it nostalgia or whatever you want, but I do truly think that Gen 5 had the worst looking pokemon. Every generation has their durpy pokemon, but I just never felt like Gen 5 had any really great pokemon to make up for that. The only pokemon I really liked were Zekrom, and the bug pokemon, which is strange, because I usually hate big pokemon. The starters were lame, the legendaries other than Reshiram and Zekrom were lame, even the dragon pokemon was pretty lame. Although, they made up for it by making the story alot better, and adding in a bunch of cool new features. Not to mention that the setting was amazing as well.