Calabi-Yau Disentanglers- Use strange attractors to unravel dimensional folds. Could be used as a weapon to create Plank temporal superstrings and harness their gravity as gravitons to make shear or as a defense in that you could use that short lived supergravity to move. Or it could be used for other things as well, I suppose, such as:
Cloak; The harnessed Supergravity causes light to bend around your ship, as long as its Schwarzschild radius is large enough.
Scan; The unfolded dimensional branes are effected by the quantum gravitic phenomenon of enemy ships and planets despite their attempts to cloak it in this universe.
An idea, in other words, that can go any way that you want it. It almost sounds like a special research option. I do not know how that would work.

Update:

*added Quasisonar Dish and Bioplasm Reactor
*added Superstring Manipulator from Malachilupus's suggestion
*added Charged Grapple Launcher and Dark Mist Shield from Fralo's suggestions

Yay... Sounds good.

Update:
*added Syncopated Pilot Console
*added Zepther TEMPEST Controller

If anyone has more suggestions, I will create modules for them.

Update:
*added modules from recent mission chains
*separated the Independent category into ship upgrades and new systems

Go ahead and give some ideas for what I should make next.

Update:
*added Vector Modification Grid (independent- upgrade)
*added Multiform Elocation System (independent- upgrade)
*added Point-Defense Cannon (independent- system)
*added Dominion Insignia (badge rewards)

I know it's long but you can check through the first post for inspiration.
Still accepting ideas for more superior modules.

Update:
*added Arberion Filter (new races)
*added Warp Jammer (made from suggestions)

With a significant time elapsed from my last post, I am hoping for some new ideas to expand my already-extensive list.
You can use these ideas to fuel your own inventions if you want.