The
Wiki has a great list of files and instructions on how to install the mods.
Check out the post I created for some information on how to install FSPort. Put basically to run it without the launcher, dump the FSPORT2_3 package into the root directory of your freespace 2 install.
"C:\Games\Freespace2"
Geh.. The Wiki explains how to run mods with FS2_Open better than I can.
To make FS2_Open work, basically grab the latest revision and place it in your root Freespace 2 directory, along with the launcher. Then launch FS2_Open with the launcher, as it'll set up the flags accordingly.
One note, It's highly reccomended NOT to run FS2_Open with the Inferno mod. I tried it and I'd crash out here and there with no warning, and sometimes I'd crash out with a FRED error of some type. Though if you run Inferno without the FS2_Open launcher, it should work.
Oh and just a heads-up, Make a new pilot profile for each and every mod you plan to run, saves you the headache of having to reset your progress in certain situations. For example make a pilot for plain freespace 2 with no mods, a pilot for inferno, a pilot for FS2_open regular FS2 campaign, a pilot for FSPORT...
I'm sure the people who know much more than I about this would have better ways to do this but this is how I've gotten away with less headaches.