Hi bears0, thank you for your reply.
To sum up my project, I have a vb.net application that communicates with a database to validate if every board in the production line is good. We use the arduino to read sensors and activate relays to validate/block the production if anything goes wrong.
bears0:
Do you absolutely need mouse control? there are some programmable keyboard emulators that pentesters use and may work for your situation.
I wanted to use mouse/keyboard to automatically chose a program on the Win2K machine so that there is less chances for human error. Mouse control would be best, keyboard if it's the only option.
bears0:
I'm going to look around now and see if there's some that can be activated with a button press or if this could be done on an arduino.
The project must be done on an arduino to control relays and read sensors. The project is based on an arduino and vb.net application.
Can it be timed or does it need human interaction? if the latter, do you want it to be wireless?
I use a scanner to scan a barcode on the vb.net app. The app sends a command to the arduino, the arduino uses mouse/keyboard libraries to automatically chose a program on the Win2K machine. The arduino communicates to the PC via Serial port with a RS232 shield. So human interaction it is.
I know it's hard to abandon your progress in something you've been working on but if there's a ready made solution it's definitely worth looking into.
I can't abandon what I've done lol. It works on every other machines I have. It's just that one machine that has the old Win2K system where I'm trying to implement the project.
Also, consider completely backing up the machine as it seems that it's quite important it stays working. 
Don't worry, we already have backup hard drives!
Here is an HID simulator which will work for Leonardo.
I have already found this.
The mouse and keyboard objets in the Arduino librairies already use HID objects to control the mouse or keyboard. It works fine on recent OS but I can't get it to work on Win2K.
Your links are interesting, but I really need the Arduino for the project. It is a key element.
Santa