I redid the Nubus connector on a SCSI card I wanted to keep because a couple pins broke off. I desoldered each pin one at a time with a cheap radioshack desoldering gun (has a suction cup on the back to remove the molten solder, the tip goes over the pin and heats it).

If I had a good temperature controlled hot air gun that would probably been quicker and easier to use.

Some people just use a blow torch and yank parts off (I guess if the old donor card is going to be junked its not too bad).