@WaffulMann you foget all the logic suggestions about XOR, NOR, NAND, more complex things like a native RAM, ...
Antennas + remote control/logic
Block Sized letters (display block or billboard block)
Hyperspeed suggestions like Highways instead of gates (dunno if you want include suggestions which are not too popular)
http://starmadedock.net/threads/highways-between-gates-how-to-make-good-animations.3310/ (3 likes/agrees)
Site suggestions:
A simple block Editor for things like
++ ++ ++
+ 1122 + 2 Letters in one Tile
+ 1122 + Tile-Editor
++ ++ ++
A "General Question Forum" to keep others clean from <3 reply threads (author can move a thread >3 replys out there (once) and into other forums (suggestions/general-discussion) without admin).
I also support organic ships.
And modular ships (I know we have copy&paste, but sometimes you just want to move a room left/right or front/rear on a deck before you build the next)
Pistons or slide-blocks which are essentially moving docking blocks.
Personalizing Star-system names.
In X-Series systems have names like "Argon Prime", "Omicron Lyre" or "Priesters Gnade" ...
In StarTrek there are Quadrants instead of +/- sectors : "Alpha Quadrant", "Delta-Quadrant" ...
A way to draw very transparent named tunnels and spheres between sectors and around objects to aid navigation.
Readable by faction members.