Wing Commander editing legend HCl was reminiscing about his work on WC Academy, which ranged from minor tweaks (replacing a single ship) to more extensive EXE diving. Two patches from 1997 really stood out, adding some cool new features. If you can't find your copy anywhere, a digital copy is just $5.99 at Good Old Games.
Drakhai patch: wca-drak.zip
This was basically an attempt of re-incorporating the Drakhai back into WCA. Copy the INTEL.* ships to the GAMEDAT folder, and DRAKHAI.EXE to the main game folder. Launch the game via DRAKHAI.EXE and something very cool happens: you can now select level 5 difficulty, which triggers Drakhai behavior: more resilient ships, the AI taunts you at the beginning of the encounter, and after enough damage, they will actually try to escape. Even the music changes when the encounter begins, which was actually a side effect of the patch and I thought it was pretty amazing :)
Multiple Friendlies patch: wca-f.zip
Ok, for this one, leave the INTEL.* files in GAMEDAT from the previous patch where they are, you will need them. Also backup WCA.EXE before unzipping the file, since it will be replaced by a patched version. Afterwards, launch IFF.EXE (at least once per Dosbox session), and then run the modified WCA.EXE afterwards. If the game hangs when entering combat, you forgot to run IFF.EXE (made that mistake last night myself when giving this a shot)
This patch is an extension of the previous one. Basically we have levels 1-4, plus level 5 for Drakhai! But.... what about friendlies? This patch allows you to select a "Level 0" skill level, which (from memory) is equivalent to Level 4, but allows you to have human pilots on your side. So you can have more complex scenarios: put a few friendly broadswords making torpedo runs on a few Ralatha cruisers, while you escort them on a lighter ship.
As an aside, this patch removes the default "friendly" setting of the Human Station, so if you have a station as Level 1-4, it will be considered an enemy.