1) They ask. Then make contract arrangements.
2) Somebody usually has the rights even if the original company is defunct. See 1.
3) Most companies are probably in it for the money. Some have way too much of that already and prefer to sit on their pretty little behinds with their gems of olden days safely tucked away.
4) This information is not and should not be publicly available.

Just to expand on 3:
Some companies don't like the idea of DRM free games, even when we are talking about some very old games.

Also, if companies have other ways of making money off their old games, they might not be so keen on putting them here. See for instance Revolution and the first Broken Sword. It's being remade for the DS and Wii, and maybe people would be less eager to buy these new versions if the original was available here for $5.99.

Apart from that, the whole concept of making point'n'click adventures for platforms like DS and Wii is atrocious :-(

money makes the world go round.

Errr.... Let's not be so vicious. There have definitely been some great point-and-clickers for the DS. Most notably, Hotel Dusk: Room 215, which is one of the best adventures I've played on any platform. It looks like the Broken Sword remakes turned out alright, as well.
Eurogamer actually did a great interview with GOG a little bit ago which goes into some detail on the process: http://www.eurogamer.net/articles/good-old-games-interview

Yeah, the DS works well enough. The Wii, though.... every single game I've tried where the Wiimote has been used as a mouse is just a slow, painful mess to control. Maybe the Motion Plus thing will help, but TBH I doubt it. Whenever I see someone shouting "point & click? that's PERFECT for the Wii", I feel like throwing my Wiimote at them....

We're definitely in agreement there. The IR response speed is too slow and the cursor too "fat" to be ideal, plus the low screen resolution doesn't help either. That said, non P&C adventures, like Shadow of Destiny, would certainly do fine.

Okay, then let me elaborate slightly: the whole concept of making point'n'click adventures for platforms like DS and Wii, at the expense of the PC, is atrocious. I'm not saying it has to make sense, it's just the way I feel. And I know I'm prejudiced about Nintendo products.

it's magic.

"Any sufficiently analyzed magic is indistinguishable from science!"

Never believe it's not so.

But whoever bought the DS or Wii version of an old pc game thinking they are buying them both versions, is gonna be sorely dissapointed. The DS/Wii versions are going to be completely different games, and their quality will be independent of the original game's quality. Most of the time the console versions will be made by a completely different dev team, completely different to the one that made the original computer game. It's gonna be a different game with the old name for merchandising purposes only. I dont think there's any relation between an old computer game, and any contemporary console version, which wont be a remake, but a complete new different title.

Broken Sword at least is an exception, though I'm not sure where your generalization really comes from. I can think of plenty of faithful updates to old games.