Metroid wins this handily for me, despite my beloved Wind Waker being in the mix. Metroid Prime is in my top 10 favorite games of all time. The only other games that rank that high for me this entire decade are Majora's Mask and Bioshock... and I like Prime better than both.
WInd Waker was great (if a bit unfinished feeling), REmake was fantastic and I loved Eternal Darkness. Oh, and Splinter Cell was incredible; showed Metal Gear how it's done on the first try.