Something I find helps make bosses memorable, even if their fights aren't that interesting, is if every boss has a place in the story. Not Giant Space Flees out of Nowhere, guys, because those just bog down the pacing.
It makes much more sense for me to fight a chimera that was previously stated in the story as being the ancient guardian of these ruins, set there by the main characters parents to never let anyone discover their dark secrets, than it does for me to fight a pair of crows that just happened to be near that plot device i needed to unlock more story.
In short, make the bosses mean something to the story, give them a reason to be there, rather than just putting something there because you need some sort of boss. This alone will help make your bosses more memorable.
EDIT: And I see Whitesphere above me just said the same thing, so TVTROPES PEOPLE UNITE! YAH!