I can't say the best, but my favourite go something like this:
1. Skies of Arcadia
2. Final Fantasy 8
3. Ocarina of Time
4. Super Mario Bros 3
5. Civilization 2
6. Xenogears
7. Terranigma
8. Dragon Quest 5
9. Earthbound
10. Chrono Trigger
If I was to say the best game of all time, the game that made the biggest splash; Pokemon could be correct, but Super Mario Bros 3 and Ocarina of Time also made large splashes. I can't say anything of this gens games until I see which ones I still play years after the end of this generation. What I can say is that last gen was disappointing to me; unless you include Dreamcast in with the generation (I kind of see it as between the PSX and PS2 generations) Xenosaga Episode 3 was the only game I really loved, possibly followed by Vice City.