The 130A is the 3G Mustang alt. It is internally regulated, small case, w/no external fan. If you need to replace the regulator it's virtually impossible w/out removing the alt from the truck.
The 100A large-case Ford alt is externally regulated w/an external fan. The large case will run cooler and the larger bearings tend to last longer. The external regulator is easily replaced on the trail if need be. If you look at any HD truck it'll use a large case alt.
I differ from Steve as idle ouput is very important to me. At least 1/2 of each trailride is spent at idle for me. The other 1/2 rarely sees above 2k, oftemtimes w/the a/c blasting in Moab. If you need to run lots of exterior lights during night 'wheeling, maybe to hook up a strap, stack rocks or to winch idle ouput is paramount.
Every alt will become less effecient as it heats up, this is why serious alt builders rate their alts at "hot" and "cold." I think for truck use (at least the way I use my truck) the large case is the way to go.
If you do a lot of desert running you've got plenty of airflow to help keep the 3G cool. Or w/bogging you've got plenty of RPM's so idle output is not such an issue. Otherwise, I think the 3G is an over-rated alt, not to mention generally more costly - most 3G rebuilds I've seen run at least $130, while the large-case can be had for about $100 (plus about $15 for an external regulator).
There's always other options, GM has a 95amp large case which is supposed to be great, too. Later Broncos w/the tow package did come w 95/100A alts but their side-bolt design makes them hard to retrofit to older motors.
See also: http://soderblom.net/bronco/tech/largealt/