Well I'm quite a fan of underdogs, so Marvel wise my fave heroes would be AOA Blink, Gravity and Nate Grey (X-Man) and villains are Xorn/magneto, Holocaust/nemesis and Mr sinister (quite X-Men-centric I know)
Dc wise heroes: Nightwing, Superboy (post crisis, pre new 52) and Booster Gold. Villains, Deathstroke, Cyborg (Hank Henshaw) and Darkseid.
I'd love to say they are reflected in my minimate collection, but out of all of them I only have Blink (which I got scalped on),Booster and Cyborg, I wasn't blown away with the DC 'mates so I cherry picked quite a bit and with the marvel side I just have limited funds, I do have the AOA Sinister to complete my AOA collection though.