I've never read the books. Sorry. But I do have autographed copies!
Don't know anything about the fan-made WC games and mods. Tell me more!
Sure.
There are many Fan-Projects to tell you about, so I hope that I don't write too much text and too many links.
Unknown Enemy and Standoff are Add-Ons/Mods for WC: Secret Ops. Unknown Enemy takes place during Prophecy and you're a Pilot of the Union of Border Worlds (Johann Daniels), as you fight Kilrathi pirates and an ivasion by the Nephilim (the bugs from Prophecy).
In Standoff you participate in the events of the novel Fleet Action, but not as Blair, Bondarevski or other familiar WC Characters, but as another new character, William Bradshaw. The Kilrathi and Confed have signed a truce and Confed decomissions most of its fleet. But the Kilrathi break the truce and head straight for Earth.
http://unknownenemy.solsector.net/
http://standoff.solsector.net/
There's another SO-based one, which hasn't been released yet: Collateral Damage:
https://www.wcnews.com/chatzone/threads/wc-cd-fan-input.24002/page-19#post-371302
Wing Commander Saga: The Darkest Dawn takes place during WC3. In this game, which is based on a modified version of the engine of Freespace 2, you are a new pilot, David "Sandman" Markham. You take place in events, which would eventually lead into the events of WC3. Beautiful graphics, fun gameplay, professional voice acting, a believable storyline (+prologue) and much more expect you.
http://www.wcsaga.com/
There are mods for WCS in progress, most notably Aginor's Kilrathi-Mod, Kevin Caccamo's Hostile Frontier (which is based on the novel False Colors), ScoobyDoo's ships and Deathsnake's Enigma 2666 (a WC2 remake but the missions are a bit different)
http://www.hard-light.net/forums/index.php?board=46.0
https://www.wcnews.com/chatzone/threads/kilrathi-interior-designer-needed.26078/
https://www.wcnews.com/chatzone/threads/some-models.25041/page-5#post-378288
WC: Invasion is a modification for Star Wars: Empire at War - Forces of Corruption, a Real-Time Strategy game. You command your Confed, Kilrathi or Nephilim ships from the bird's eye view:
http://www.moddb.com/mods/wing-commander-invasion
Privateer Gemini Gold is a remake of WC: Privateer, based on Vega Strike's engine. This is a space trading game, in which you fly your ships, buy and sell things, accept missions and fight enemies like Pirates, the Kilrathi, Confed, Militias, Hunters and the Church of Man (aka Retros):
http://privateer.sourceforge.net/