I think MGS stands out in this category. Every boss fight is different and fun in it own way. Sure there are some standout ones (Psycho Mantis) that maybe pull ahead of the others, but the fact that every boss fight plays out differently is one of the great aspects of the game. And yeah, that certainly extends to the whole series, but I think it's particularly applicable to the first one (not to diminish from creative fights, like The End in MGS3, but I just don't think the other games match MGS in terms of the bosses as a whole).

I think the Megaman series (at least the good ones) fit this topic too. The games are all about the bosses in a way, so the good ones definitely have good boss fights, even if they lack the diversity of MGS (yeah, I'd definitely rank MGS higher but Megaman gets an honorable mention).