Looks like I'm late jumping into this one but I just noticed it. I'm another Zappa nut who owns the entire Verve catalog and roughly 45 releases overall. Most of his best has already been listed here, but I wanted to add a few thoughts.
Of more recent releases, both "Make a Jazz Noise Here" and "Best Band You Never Heard in Your Life" are astounding live performances (minus a little between song goofiness). "Roxy & Elsewhere" remains an all-time favorite. I'd love to see that one re-issued on heavyweight vinyl.
Jazz fans will likely enjoy the version of "Let's Move to Cleveland" found on Volume 4 of the "You Can't Do That On Stage" series - it features Archie Shepp on tenor!
Two other recent relases of Zappa material by other artists are welll worth it. The Persuasions relased "Frankly A Capella" on the EarthBeat! lable in 2000, very nicely done all-vocal renditions done with heartfelt feeling. And the "Ed Palermo Big Band Plays the Music of Frank Zappa" was released on Astor Place records in 1997 (well, I guess not that recent).
An incredible enigma of an artist!