I'm looking for some games that have cool bonuses. I see that Retro City Rampage has a printable doorhanger and a papercraft, Carmageddon Max Pack has papercraft cars, and Far Cry 2 has a making-of video, but what else is there?

phantasmagoria 2

I'd say the Witcher games probably have the most and best extras.

Of the games I own here on GOG, the ones with the best extras, in my opinion, are:

- Alan Wake (and, to an extent, Alan Wake's American Nightmare);
- Bad Mojo Redux;
- Beneath A Steel Sky (comic book by Dave Gibbons and the recently added Security Manuals);
- Broken Sword II: The Smoking Mirror Remastered (basically because it has the original game as an extra);
- The three classic Fallouts;
- I Have No Mouth And I Must Scream (the original short story by Harlan Ellison?! Hell, yeah!);
- Oddworld: Stranger's Wrath HD (same as with Broken Sword II, every remake/re-master of a classic game that includes the classic one as an extra is a win in my book);
- System Shock 2;
- Wing Commander III: Heart of the Tiger;
- The Witcher Enhanced Edition: Director's Cut;
- The Witcher 2: Assassins of Kings Enhanced Edition;

Obviously, there are lots more, but it's easier for me to stick to the ones I actually own and whose extras seem to be better.

Alone in the Dark has three extra games as extras :P

I'm not sure if this is quite what you're asking for (it seems like you're looking for extras that are in some way weird or unusual things to have as an extra), but there are a few games on GOG where the included materials (manuals, reference guides, inserts, etc) really go above and beyond the call of duty in acting as an extension of the game world and immersing you in the theme. A few examples include:
-Arcanum - Of Steamworks and Magick Obscura: probably the greatest game manual ever, it has extended (and entertaining) essays on the game universe and its races delivered as a series of antiquated science lectures. If you love the game but haven't checked out the manual, you're missing out.
-Wing Commander 1 + 2: Many of the reference materials are written as newsletters and manuals that would be handed out to actual crew members aboard the ship. (Later Wing Commander games may continue the trend, but I wouldn't know since I haven't gotten to them yet.)
-Crusader - No Remorse: Similarly, many of the equipment guides and other materials are presented as intel stolen from the Consortium's databases by hackers, and contain numerous margin-notes from the in-game characters.
-The Fallout games (may the rest in peace) - all the little PipBoy cartoons in the manuals do a great job of establishing the games' discordant blend of 1950's chipperness with post-apocalyptic misery.
-I Have No Mouth And I Must Scream comes with a copy of the short story the game is based on.
-"Divine Divinity" includes a full prequel novella that sets up the game's events. (Unfortunately, it's quite terrible.)

There are also some games that I consider worth it for the soundtrack alone, including Thunderscape, Entomorph, and Chaos Overlords.

Finally, Roman5 has a GOGMix of games that come packed with tons of extras: http://www.gog.com/mix/incredible_value_gogs_with_a_huge_list_of_extras

Uplink comes with the source code.

Don't miss out on the GOG-exclusive DOS-Deluxe Edition: Make P2 look like a Sin City movie, thanks to a broken color palette - now with even more scanlines!

I would add Papers, Please to the list: it has two small, extra games included (okay, they're freeware but this saves you the trouble of finding them on your own; besides, you might not even know of them if they weren't included as extras)

I'd have to say <span class="bold">The Witcher 2</span> hands down as the game plus extras totals in at 25.8GB and comes essentially with the kitchen sink, including a nice playboy spread of Geralt's babe Triss. ;o)

Flight of the Amazon Queen.

http://www.gog.com/forum/flight_of_the_amazon_queen/be_sure_you_check_out_the_making_of

MORONS!

Carmageddon comes with fold up paper cars so sit on it! :D

Earth 2140 and Wizardry 7 come with the original superior DOS versions.

they said extras and not the main game. Though that doesn't bother me in the slightest.

IL-2 has a nerdtastic aircraft guide that I've spent countless hours reading.