Last Scenario is a pretty good game, with classic turn-based JRPG mechanics.
La-Mulana has been mentioned quite often I'm sure, but it's still one of the best metroidvania type games.
Ark22 is a zelda-like, as far as I know, but haven't played much of it myself yet.
As for non-free games, the Tales of Destiny PS2 remake is a pretty great mix of beat 'em up (some features could be likened to Guardian Heroes) and RPG, using an altered version of the LMBS. It's Japanese, but there's a fairly complete
menu translation. [/shameless plug] You might wish to wait for the director's cut version, though.
Also, some Castlevania games, Rondo of Blood and Symphony of the Night, in particular. Yeah, obvious choices, but whatever.