I'm looking for this a bit old game that was really fun but I can't seem to remember its name. It was old but not too old, I think 1995-2000 probably.
here are a few elements of what I can remember :
-you were this guy trapped in a factory I think, where a gas or something transformed everybody else into hideous monsters
-the action was set "in the future", and I think the year they mentioned was 2009 lol
-it was 2D, puzzle - like, kinda like Gateworld, with going from different places to another, trying to open doors, shoot the bad guys etc
-the character was black, not as the race, black as in you couldn't see his face because of the breathing mask, and he looked all black-dressed and designed
-the game had a grey/black look, sort of creepy
Any reply is more than welcome, thank you

The setting and character match "Abuse" - mobygames link here.
Blurb from Mobygames follows:
"It is the unimaginably distant year 2009. You are Nick Vrenna, falsely locked inside a high security prison. The genetic experiments conducted in the prison, combined with a full-scale riot that took place recently, caused all guards and inmates to be transformed into insane, aggressive mutants. Your job is to escape while stopping the genetic plague from transforming the whole world."
If this is the game, you should be able to find a full version to download without too much hassle. Unfortunately many of the Abuse fan pages have folded, and this is the only project that looks active. There are links to other sites near the bottom of the project's index page.

If that's the game, Dotemu has the full game GOG-ified for XP/Vista/7 32/64-bit...free to download, of course.
http://www.dotemu.com/en/download-game/79/abuse

that's it, thank you enormously

I've downloaded it from there, but it's just shareware, 4 levels only (which I finished in less than 1h :D )
do you know of other sites where I could find the full version of the game?

That's quite strage because Abuse is a Freeware (not abandonware). I think that if you google for it a bit, you should find a link to the complete version quite easely.

See how bad I am at guessing, I would have guessed Bio Menace...

Unfortunately the release status of Abuse is complicated.
The original authors, Jonathan Clark and Dave Taylor, released the source code and shareware levels as public domain (source). The author of the sound effects also agreed to let them be redistributed (whether implicitly or explicitly is not clear).
The fact that only the shareware levels were included spawned a whole project to compile fan-made levels, called "frabs". If you find a copy of "frabs" for download, its levels are probably different to the full version of Abuse.
There was a project for a short while named "Abuse32" which appears to work on Windows XP, but not on any more recent operating systems like Windows Vista / 7. This version might include the level set from the original full game.
The current linux/mac port indicates that the original authors have allowed the full levels set to be "freely redistributed for Abuse-SDL". This is not the same as releasing the full level set as freeware.
Unfortunately, there is no Windows build of this port, so you can't simply download anything from that site and get up and running. It may be possible to just copy the full level set ("abuse-data-2.00.tar.gz") into a working copy of Abuse like the one from DotEmu, but this seems unlikely.