Single most important mod - the "Freedom Force X", which already has a separate thread, so I won't go into further details.
http://ffx.freedomforceforever.com/manual.htm
"Pulp Fiction", old-school themed expansion,
http://www.alexff.com/downloads/pfffvttr.exe
"Patriot City" - a free-roaming mod.
http://www.fundamentzero.com/patcity/index.htm
"The Strangers 2" - a new campaign.
http://www.fundamentzero.com/strangers2/index.htm
Special bonus:
The main forum for all things FF:
http://freedomreborn.net/simple/index.php
Global hub of various FF stuff:
http://www.freedomforceforever.com/

Note: The Strangers 2 was a cancelled mod project for the first FF game.* But there are plenty of other available.
*Try to get your hands on the first game. The Strangers 1 and Dr. Mike's other mods make it worthwhile by themselves – and there are quite a few other great mods for it.

Howdy folks! The FF community has moved, and you can now find us at:

http://freedomreborn.net/forums/index.php

Also, you can find my set of mods here:
http://bentongrey.wordpress.com/
Those include my DC Universe mod, my TMNT mod, my Project Superpowers mod, and more!

Pulp fiction mod will not install to the GOG version of FF v TR,I get a cannot create uninstall message and the install stops.

Hi Dudalb, sorry for your trouble! I'm afraid I don't know about that mod's quirks, but you might try asking for help at www.freedomreborn.net. That's the home of the FF community, and there are a lot of knowledgeable folks there.