Full explanations on all SEXP's and TBL flags.
Remove "player must be Alpha 1" restriction
Ships that can't be given valid orders don't show up on the Orders list.
Ability to alter the level and coloring of ambient light in a mission?
I second Venom's camera size reduction.
"Copy background data from..." option in FRED2 which selects a file and copies it's nebula, star amount, asteriod field and jumpnode data to the clipboard, available to be pasted into the current mission.
Preview window in the Background editor
Dropping (or passing as parameter on command-line) a mission file onto a FS2.exe shortcut loads up that mission.
Same as above with FRED2; double-clicking on mission opens it in the editor.
Better rendering of nebulae in FRED2.
Correct positioning of HUD and game interface in (along?) Z-buffer to allow playability with 3D glasses.
Any and all game-related material? ie. terran, Vasudan and Shivan 3D models, "scientific" explanations of subspace (travel time, entry and exit directions, etc), explanation of lack of radio contact between Sol and the GTVA, etc.
And most of all: don't give us these package deals of Freespace 1+2 for $20... we want Freespace 1+2=3!!!!

*runs and hides*
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America, stand assured that Israel
truly understands what you are going through.
"He who laughs last thinks slowest."
"Just becase you're paranoid doesn't mean they're not out to get you."
"To err is human; to really screw up you need a computer."
Creator of the
Sandvich Bar, the CapShip Turret Upgrade, the Complete FS2 Ship List and the System Backgrounds List (all available from the site)