A heat gun to preheat the evil ground and power planes in these boards is pretty much crucial. You're usually good below 700F for as long as it takes to bring the source side of the board up to temp since most through-hole parts like caps are wave-soldered. If there are hand-soldered through-hole parts in place, those were hand-soldered because they will melt in the wave tunnel. Yeah, stay away from those with the heat.
With the preheat, you should have no trouble cleaning the hole. If you do, just do like me and use a wide tip on your iron to melt the solder in both holes at the same time and feed the new cap through to push the solder out of the way.
I use a Hakko iron, personally, but there are a lot of choices. Metcal for the dead-serious, for one.
-- I'm a PeeCee and I can kick your ass. --
Slow PeeCee - i7 940 OC 4.1GHz, 20GB DDR3 OC 1.8GHz, 2x1TB WD RAID0, ATI 5870 1GB, 3008WFP
Dev PeeCee - IBM Intellistation A Pro - Dual Opteron 290 2.8GHz, 8GB ECC DDR, 500GB SATA, 8400GS, 2x1800FP
Slow PeeCee Cluster - 30x Opteron 275, 60.5GB RAM, 2.2TB, 2x1.5TB
Octane 2xR12K-300, 1.5GB, 36GB 10K, 73GB 10K, V8
Indigo2 195MHz, 1GB, 36GB, SI
There are 10 kinds of people in the world:
Those who understand Ternary. Those who don't. Those who could give a shit less.