I have been collecting a decent sized force of superhero figs over the last few years but have struggled to find really good villains outside of the Heroclix line. The main problem with using well known villains in a superhero RPG is that invariably somebody in the group knows pretty much exactly how to defeat them based on 60-70 years of comic history so even if the main mastermind villain is Apocalypse or Vandal Savage I prefer to have most of the baddies doing the fighting being new or original characters that my player's won't be familiar with.
Luckily Reaper (again their excellent Chronoscope line) and Comfy Chair Games have produced a couple of awesome "brick" type baddies for use in superhero games. These type of guys don't have very complicated power sets but when you need to punch a hero through a wall or throw a car at somebody they definitely fit the bill.
It definitely looks like clobberin' time.
This guy looks like he has old-school underwater mines for fists!
(Comfy Chair Games)
This guy has nodes for inserting chemical vials all down his back.