The Steam version of System Shock 2 is DRM-free.

Serious Sam Classic First and Second Encounter are both DRM-free.

You can add Arcen's entire catalog to that list.

AI War: Fleet Command and all of its expansions.
A Valley Without Wind 1 & 2
Shattered Haven
Skyward Collapse

Are Arcen's games on steam patched via steam or natively?

Via Steam.

It isn't out-of-the box drm-free, but Fallout 3 with FOSE can be run without Steam. Windows Live is automatically disabled by FOSE, and by running Fallout 3 with the fose launcher, it negates steam. If you have Fallout 3 on steam, you probably install some mods, and since many mods require fose, you can probably run Fallout 3 without DRM.

hm... might test if it the same for Skyrim...

I guess it will be classified as an hack, though.

I'm quite sure it isn't. Fallout 3's launcher requires Steam, the main game executable doesn't, and FOSE doesn't run the launcher (you can just as well make a shortcut directly to the main exe, if you don't use any mods that require FOSE - though GFWL is still active then). Skyrim's main executable didn't require Steam originally, but that was quickly patched (the launcher always did).

Their games have in-game updater too, that you can get all beta and official updates through. You can set Steam to never update the game and do it yourself, or you can keep up with the betas with the in-game updater and just let Steam push the updates to you. Or you can install the games through Steam, then put the folders wherever you want, uninstall Steam and play them like any other DRM free game.