I know of two designers based on BattleSpace:
http://www.pryderockindustries.com/dl_misc.php#BS - this is a DOS program. Seriously. ;)
http://www.pryderockindustries.com/dl_misc.php#BSXLS - this is an excel spreadsheet
Both of these are designed for BattleSpace.
HMA is the only program of any kind that I know of designed for AT2. Seriously, the design rules are so complex that almost nobody has the patience to deal with them all the way through. I've heard rumors of a dozen programs, only HMA has made it out of development hell. ;)
There is as yet no program designed for Total Warfare-era rules, but as those rules are mainly based on AT2, it is easy to use HMA for them. In short, the ONLY thing I've had an issue with so far is placing subcap weapons on DropShips. For that I had to enter them in as cap missiles. Also, the mass drivers have to be entered in as two weapons because HMA just doesn't have a capacity for allowing weapons that do more than 100 points of capital damage... ;)
Still, I have designed every single canon large ship (except some of them in the XTROs that I don't have yet) in HMA and it works. :)