Whitch MODS are in Progress??

Well, you've got the Balance Mod, which is basically stock only better, with some improved AI to boot.
Then you've got the Interrelations Mod which revamps the tech tree, and features some pretty agressive AI.
There's also the GrittyGalaxy mod which is kind of hard to explain, but a whole lot of fun. There's no functioning AI for it at present, so it's multiplayer only if you want any challenge.
Then there's the Golden Eclipse mod, which features an entirely new tech tree, and lots of new art and sounds.
And then there's the FQM which is essentially stock with a whole bunch of fancy graphics & graphical improvements, though it's also been incorporated into the Balance Mod.
There's probably a lot more in the works, but those are the big ones I know of that have at been released in any shape or form, and they can all be downloaded from: http://www.spaceempires.net/home/downloads-cat-35.html

Suction feet are not to be trifled with!

FQM is also incorporated into IRM...

There is also the Ground Combat Mod, but I know little about it. It does seem to still be in development.

Both Gritty Galaxy and Golden Eclipse do not appear to be in (as) active development as the others.

Javaslinger

Well Me and Isopco are working on a BSG mod. Works been a bit slow since 1.33, but it will be out at somepoint.

Any plans for adding the Rage? the Vaxin?

My personal mod is always in progress, though I doubt I will release it to the public.