Well there's Jetfighter...

http://www.gog.com/wishlist/games/jetfighter
http://www.gog.com/wishlist/games/jetfighter_ii_advanced_tactical_fighter
http://www.gog.com/wishlist/games/jetfighter_iii

Jetfighter is an action/sim concentrating more on the fun of flying and missions rather than trying to be realistic (although having too low of thrust or going too high will stall). An early example of a 3D game that aged rather well, although the original one only used 4/16 colors.

The Enchanted Cave 2

http://www.gog.com/wishlist/games/the_enchanted_cave_2

Based on the original flash game, you traverse the cave. It's a rouge-lite pushing for resource management, and knowing when to quit or if you can push for how far you can get. Often you can leave at any time but certain items you'd have to leave behind vs selling at the shops on floors. In some ways it's almost zen-like to play for a few hours at a time.

<span class="bold">Genewars</span>

It's a real time strategy by Bullfrog. A technologically advanced alien race has forced 4 warring alien nations to cease all warfare and start "restoring" planets that where destroyed during the conflict. Each mission you select a team of specialists (engineers, herder, botanists... etc) and start on a planet were you have to establish a base and reach an objective (e.g. create x number of animals or destroy all other teams). There are 4 races with different abilities, but each player actually gets to pick specialists from different races, so you can have all humans or a mix of all races. Your "forces" consist of animals that can be genetically mixed, so you have mules who are good at menial labour and work like... well, mules. And crabs who are good fighters, and you can combine them in a genetics lab to create crabomules or mulocrabs, each with different abilites. If you do well, the overseer alines reward you with special monoliths that you can use to improve your specialists or creatures. If you destroy the planet too much, they can start attacking you too, which can be painful, since you can't really retaliate.

Wishlist entry
http://www.gog.com/wishlist/games/genewars (211 votes) I got this on CD back when it came out and though I'd love it since I'm a big RTS fan. However I gave up after a few missions. My biggest issue was lack of good story, and the fact that unlike e.g. Warcraft 2 where units are very varied, all submarines look just like... submarines. The depth was a nice addition, but controlling units to make full use of this feature took some getting used to.
Still maybe I judged it too harshly. I'll see if I can give it another try some time. Voted for the wishlist.

They are both the same game, but one entry was misspelled. The right name is <i>"The D<span class="bold">ae</span>dalus Encounter"</i>. I've updated my post. Thanks! ;-)

Gender Wars (167 votes at the moment)

A damned silly RTS which indulges in cartoonishly broad stereotypes of both genders. You can play either side, though both are ultimately doomed, given the nature of their conflict. ;)

Like my earlier post (Millenia: Altered Destinies), this is one I still own on CD.

I second that, this game has all the Gobliiins strengthens - cartoonist humor and super challenging puzzles plus a real back story and plot (that despite the aforementioned humor could be quit serious) and an open world where the player could travel as he wish rather than the level structure of the Gobliiins series (or for that matter all of Coktel Vision games).

Woodruff is one of the best and most challenging quests I played and the best game created by Coktel Vision.

According to two articles from "PC Welt", the first MadTV was indeed released as freeware in October 2001, but only for a limited time (one month). The second one followed in November of that year, under the same condition. Of course, I don't know how much of this was strictly legal back then.

And then somebody made a spiritual successor called "M.U.D. TV". I'll do it a favour and say no more about it.

D/Generation (95 votes): http://www.gog.com/wishlist/games/dgeneration

It's a cyberpunk action/puzzle game played from an isometric perspective. You control a courier making a delivery to a highrise office building. The problem is the building's security systems have gone haywire and trapped you and a variety of innocent employees inside while deadly security mechanisms and genetic critters rampage all over. So progress is made by figuring out how to get past all the traps while hopefully leading the employees to safety (a flaw: the employees are often foolish and will get themselves killed through little fault of your own). As you go along, a little story emerges about why all this is happening.

It's a very well-designed game with attractively minimalistic graphics. Difficult but fair. Whenever I play it, I always feel compelled to play just one more room, one more floor. Whenever I see people talk about it online, it's always fondly remembered but the problem is that hardly anyone played it, so it's really fallen through the cracks and needs someone (*ahem* like GOG) to rescue it and give it the attention it deserves.

I remember playing and beating this game years and years ago... Although apparently the DOS version is a port from like the C64 or Amiga system.

God that's an old one...

My game that I will place on here is called Amber: Journeys Beyond. On the wish list there is less than 300 votes, there are 212 votes on the community wish list.

Amber Journeys Beyond is a Myst like game, point and click adventure game, developed by Hue Forest, their only game before it went under, the game didn't make commercial success since it was independent and didn't launch with a well known company, designed almost by 2 people alone. It is a horror style, and the object is to figure out the AMBER device and save your friend, and transverse 3 worlds of ghost realms to figure out their deaths. Short game, but pretty cool, came out in the DOS days and Windows 95 days. Love this game!

Amber Journey Beyond

It is a highly underrated game with battles using C&C mechanics, but what made it special was a stock market simulation that granted bonuses if you aquired over 50% of a company in some field and it had a neat research and unit design part also. Without further ado: War Inc. (80 votes)

Mace Griffin: Bounty Hunter, currently at 58 votes

Toroughly entertaining sci-fi FPS, starring Henry Rollins as Mace Griffin, with a novelty that at certain points you can take out a ship and fight in outer space.
It also has pieces of music that takes away the cake from John Barry, can't find out wether they're composed by Ian Livingstone or Dean Evans (soundtrack from Silver).

I have two:

First is Isis, which... I feel that I can safely claim has less than three hundred votes at time of writing. Specifically, it has seven.

Isis is--as best I recall it--a point-and-click adventure in vein of Myst, tasking the player with solving logic puzzles presented in pre-rendered 3D.

The setting is the interior of a pyramid, in which the player is tasked by Isis with reactivating a cosmic starship so that it may continue its journey of bringing hope and music (Earth Wind and Fire, to be specific) to the world!

It's... a little strange. ^_^

Second is Project: Inner Space, which has a slightly healthier wishlist entry at fourty-four votes at time of writing.

Project: Inner Space is a top-down shooter set in a space-like environment generated from your directory structure.
The plot, as far as I recall, involves destroying viruses and confronting the Inner Demon that guards four powerful weapons. Adding to this is a set of AI factions, each with their own tendencies of behaviour and disposition towards the other factions and to the player.

Alas, while the owners of the game do still sell it, they charge twenty-five dollars ($24.95) at the cheapest, I believe. :/

Igor: Objective Uikokahonia (Currently has 37 votes)

The first adventure game of Pendulo Studios, while the game itself is quit short, it has good humor and a good story about a geeky guy who try to score a date with the high school babe, the game also have a very Lucasarty feeling to it.

I'm not surprised that you mentioned it since you were the one who helped me finding it! As I said in that thred, it's not flawless but it should definitely be here!
I actually own that one! And yeah it is a pretty nice p&c adventure game. Nothing really special but very solid and entertaining enough to be sol here. Voted!

that actually looks pretty cool