For Aquaman it's Ocean Master or even the new/old addition The Dead King. I like Black Manta and all but I don't like Aquaman being written in a lower then avg. Setting just so Manta can challenge him. Johns wrote Aquaman villains the best in my opinion.
For Batman it becomes tricky because he's that guy who has various of really awesome villains, who present various threats. I guess I like alot of the Anti-Batmen (Wraith/Slade/Prometheus) but then again characters like Two Face, Ivy and Clayface are favorites. So pretty much the whole damn gallery. My only complaint is how Joker is handled by some writers.
For Cyborg right now it's Grid I'm really excited to see his rogue gallery grow though.
For Flash his entire Rogues gallery is awesome. My only complaint is Speed Villains seem like they might possibly become abundant.
For Green Lantern I think Johns created alot of really interesting villains when he introduced the variety of colors in the spectrum (Black Hand, Larfleeze, Atrocitus. Hands down still favorite would be Sinestro. Or Parralax Hal?
For Shazam, it's ironic because it's one of those situations where I like the main adversary more then the Protagonist. Black Adam hands down.
For Superman my favorite villain is probably Tyrell from Earth One, Superman has alot of great villains though like Lex, Doomsday and sometimes Uxas.
For Martian Manhunter it's definitely Despero but I see him as often times a League villain moreso then anything which I'm pretty sure he was introduced in JL.
For Wonder Woman, it's probably Ares or Cheetah for me. I also like Circe.