I've used specially designed assault cruisers before; slow, usually lots of armor (this was before shock damage.. does anyone know if shields stay at full power after a jump?) and a high jump distance on the jump ship, with redundant systems and usually lots of short range missiles in box launchers. The idea being for them to jump through and survive until their systems come up, then cover for other ships as they come through.
On the other hand, I stopped using them since I almost never see the AI defend a jump point. Kind of a pity, since it would add some more diverse tactical situations.