Second to reaper.
THeir chronoscope line has lots of options, but don't forget their fantasy line, There's lots of cool figs in there that could be part of inquisitorial, Rogue trader, or ecclesiasical warbands with just a few weapons swaps.
As for cheap options...
-As you noted, there's a number of good options in Mega Minaiture's "Sci-fi Salvage crew" line of miniatures. I have a number of these and the lines in that section scale perfectly well with
40k.
-Have you looked at wargames factory or Defiance games for more faceless grunts?
-East Riding Miniatures Many possibilities there.
http://shop.eastridingminiatures.co.uk/erm-25-11-c.asp
-Black Tree Design. I have some of their space dwarves and they're really nice figs
http://www.blacktreedesign.com/northamerica/home.php?xid=08b7a5f9994021d5abc29077449f6fef
-Lead Bones and some of the other ranges by recreational conflict. These scale up very well with modern figures. I have some of their hazmat troops.
http://www.recreationalconflict.com/
If you haven't settled on a ruleset yet, consider these two options.
Inquisimunda. A well regarded fan combination of Inquisitor fluff/gear and necromunda. You will need Necromunda to play.
http://empireofghosts.blogspot.com/p/inquisimunda-resources.html
In The Emperor's Name. Warband skirmish fighting in the
40k universe. Neat scenario generator and lots of force "retinue" lists. More on the fast-play end of things though.
http://thegamesshed.wordpress.com/2011/07/02/in-the-emperors-name/