Re: follow the money?
Maybe that's really why Ballmer is leaving MS. He knows he's about to get caught with his hand in the jar. I'm kidding.
It hasn't come back up much since the ridiculously tiny PRISM sum in the slides. But even with that small sum you're talking about several people per organization that would have to either be paid off, tightly controlled or maybe even NSA agents working for the companies. I suppose they could be paid off in company stock, purchased by the NSA then magicked into holdings of those involved. It's easy for employees to justify having shares of the company they work for.
It sounds rather tin-foil-hatish, but putting agents on the staff with the preconditions that they work autonomously from everyone else really wouldn't be too difficult. That tactic already has form with the AT&T leaks from a few years back. They probably wouldn't have been caught then if they hadnt basically labeled the room "Super Secret Spy Stuff Closet". The less structured environments of the companies known to be involved would make it a lot easier than an old guard company like AT&T.
The logistics of all of the money are so potentially convoluted it makes it impossible to even guess realistically on how they've been hiding it. I suppose that's why they are intelligence agencies though, they aren't supposed to get caught spying. You have to assume they're good at it.