You can make changes to ships or weapons.tbl
You could make interface art
You could make new ship textures
You could make new effects
You could make hud shield icons for all the ships in FS2
You could make new hud art
You could make new main hall art
You could make high-poly ships
You could make high-poly asteroids
You could make new species definitions
You could make better-quality music
You could make medal art (I've never seen new medals, ever)
You could make new lightning bolts
Edit: Oh, and look up VPView and QuickVP. That'll put you on squares two and three.