Ok, first of all, where do you live? I wouldn't recommend taking off any smog equipment if you live in a state that does emissions testing.
That being said, it just depends on what you want to do. I've heard that shorties provide more low-end torque and that long-tubes provide more top-end horsepower.
I'm going with some summit brand ceramic coated shorties. I'm pretty sure my truck has a Flowmaster Y-Pipe (exhaust was done by previous owner, I haven't looked at that yet). Even if it doesn't, since I live in CA, going with shorties is much easier for smog reasons than hassling with LT's. But that's just me.