Here is a good manual for recapping your motherboard from Capacitor Lab. They go a bit overboard but its a good guideline. Guide
Personally I find the fastest/easiest way to do these is to:
1. Cut the leads on the caps you are going to remove to make them easier to pop out. Cut them from the bottom of the board as close to flush as you can without damaging the board. *On the GX boards I like to bend the fins on the silver heat sync to get the 1000uF caps out; itís a lot faster than taking the heat sync off.
2. Use your soldering iron to remove all of the selected caps. I heat one lead from the bottom of the board while pushing gently on the capacitor towards the other lead then switch and the cap will fall off.
3. Then go back and clear the holes using your iron and a pump ( heat one side and suck the solder out from the other ). I also use a stainless needle to further open the holes if required.
4. Place all of the caps on the board bending the leads to hold them in place.
5. Then solder them in. This is where a hot iron comes in handy. Heat one side of the lead for a couple seconds then apply the solder to the other side of the lead and it should flow right in. Try not to touch the solder to the tip of your iron or it will probably stick to it and you will get a bad joint.
6. Run a burn in tool, I use the Dell Diagnostic disk available for download on the left.
I like a 40-45 Watt iron to remove caps and I use that or a 35Watt to solder the new ones in. You don't have to buy an expensive set, I got mine for under $20 and have done a lot of boards with it.
40 Watt Iron