Some games that are first in their series and I also think they're the best in their series (though I might still think the later games are very good):

Chrono Trigger
Blaster Master
StarTropics
Tail Concerto
Mega Man Legends (first in the sub-series, at least)
ActRaiser
Valkyrie Profile

I'm coming up with fewer of these than I expected, actually. I feel like I often buck the trend of thinking the latest game in a series is the best yet, but in many cases, I haven't played every last game in a series. I know I like Pikmin more than Pikmin 2, but I've yet to play Pikmin 3 or the handheld game. I know I like Katamari Damacy more than later Katamari games I've played, but I haven't played them all (mostly it's the mobile ones I haven't). So I can't honestly say I like the first best in those cases, even though I may suspect it would be the case if I played them all.