How can you miss them? Returning to areas to unlock previously unaccessable portions, save points, and dowsing (Prime Series). All three of those are in Metroid. I thought for sure you'd recognize those with Metroid being your second-favorite game series.
The Sonic Adventure series have a lot of sentimental value to me, especially the level "City Escape" from SAB2. Playing that in Sonic Generations really sent a shiver down my spine. And what exactly is your avatar right now?
StarFox 64 and Super Metroid are favorites of mine.
Oh, and the original Kingdom Hearts game holds some sentimental value, too.
It's definitely one of my favorites. I grew up playing that game, and did it again for old-time's sake. It's really good, except for the ending gets a little "power of friendship!" if you know what I mean.
from what I can garther FSA should be after Lttp and before LoZ