Yeah, Grey Wolves and NYGM tonnage war are the two heavy weights out there.
I don't use NYGM at the moment, but it's goal I think is to make the game as realistic as possible, and includes new crew fatigue model, ship damage (also included in GW), modified campaign, and a whole host of other things I'm not qualified to comment on. A major thing this mod does is get rid of the renown based system and now uses tonnage.
Read about it here:
NYGM Tonnage War (official thread)
As for grey wolves, apparently its the largest mod ever made for any game ever! or so I hear... it is 1.8 gb
GW includes a ton of new stuff such as sounds and textures, as well as a reworked campaign, new ships and a lot more.
I suggest you go here and download the readme:
http://www.subsim.com/phpBB/viewtopic.php?t=50034
things have come alot further since Rub.
There's also been a mod released that combines NYGM and GW here:
http://www.subsim.com/phpBB/viewtopi...r=asc&start=50
and campaign files only:
http://www.subsim.com/phpBB/viewtopic.php?t=50377
Happy choosing!