I've just install a Sunon 80mm in my case (2 wire).
I brought a molex splitter cable (one male, two females), since I didn't want to screw with the molex's on my power supply and I needed more anyway
You can use a small (very small) screwdriver to remove push the sides of the metal guides inside the molex to remove the existing wire and connector (that's the hard bit). (I took the red wire and the adjacent black, since I wanted 12v).
Once that's done, cut off the two pin connector from your fan, and solder to the top of the metal molex guides - insert them back into the molex connector and you are away.
This is a cheap way to do it, it didn't take up an existing molex, and it works well. And, I've kept my 3 pin headers free for 3 pin fans!
Kryten.