I don't know what a lot of you guys are using for strings, in terms of lower tunings, but my friend/shop owner where I take my gear recommended these:
Dunlop Manufacturing :: Strings :: :: Heavy Core NPS
I'm tuning my SC420 to D standard, and it's got a 25.1" scale neck. With the 11-50's, they feel and sound fantastic, and are not as floppy as the EB's they replaced. They also don't have the shitty feel that the Cobalts on my JS do.
If you're looking for something for lower tunings, I like 'em!
I hated'em personally! They were ok but they lost their sparkle after about a day, and didn't really feel any different from any other string in the same gauge. Felt kinda gimmicky