I was going through the fallout bible timeline a little earlier and I noticed there's almost no mention of Prewar companies. I've seen on the wiki some companies which I will use for RP inspiration, but I wanted to know if anybody knew about cool, super secret companies that are hard to find or if a big company had a secret project going on.

http://www.falloutwiki.com/Pre-War_companies?

http://www.falloutwiki.com/Greenway_Hydroponics can be an interesting choice, particularly if an employee subverted Derek Greenway's pacifist policies for his own ends. If you want a weapons-centric comapny, try http://www.falloutwiki.com/Yuma_Flats_Energy_Consortium.

Though I think that it's best to just create your own company and tie it into the existing role. If you want a real example of an evil company for inspiration, look up Chevron and its dealings in South America.

West-Tec and/or Vault-Tec

Those would be the only canon ones that come to mind.