eddieb has released several ship packs for Flight Commander. The stats included with the craft are wrong, but this adds a fresh bunch of meshes to apply and fly. The 7.5 meg combined zip includes a huge assortment of fighters, capships and bases from Wing Commander 1 through 4 and Armada. You can grab the pack here. A playable Flight Commander version is also required.
If you need assistance applying the packs, check out the Crius thread here.