At home I always use a $10 Sweex (I believe this is a local dutch el-cheapo brand) USB hub. Works fine, own power brick so it's (hopefully) not drawing any power from the PC to power the devices. This does have the consequence not being power limited I think, because I have blown 2A MOSFETs on my PICKIT2 before (bloody PICKIT software hang and accidently shorted the power output, smoke
)
If you want to 'isolate' a single USB port, you may find it convenient getting an old laptop and use that. This of course brings issues if you have 2 USB devices, because USB on the laptop still has the same ground. And working on it from the 'workstation' isn't convenient.
This also stresses the disadvantage of high-speed USB devices on USB. Like a RS-232, bus pirate and low-bandwidth thing is probably something you can run on a hub plus 12mbit isolator. A scope or logic analyzer not. Laptop for 'debugging' via scope and such only? Futhermore, how big are the odds you need your logic and scope simultaneously? (scope: signal quality, logic: protocol debugging)
I don't think a PCI-e device will work though like james suggests. There is a chance they probably don't have any fuse and will probably blow the motherboard anyway. The device is powered from the motherboard after all.
I see on many modern motherboards polyfuses now. I paid close detail on when purchasing my last PC whether they contained them, but I actually couldn't find any motherboard without. Though, I did spent 170$ or so on my MB, so I guess it *should* have some protection.
What exactly have you blown? I also played with projects at internship and college with USB. This is ofcourse on a laptop (Samsung R510 AS02) and not in my own hobby space. I shorted out the +5V to pretty much anything whilst completely messing up (and messing up the fixes!) the pin-out of an USB B connector, and the only damage I did was to my projects. All 3 ports still work.
That experience gave me so much trust in this laptop I'm not afraid of blowing it up.. At internship I didn't have the right cable for an industrial USB boxed header connector (like onboard of a MB). So I disassembled one and directly connected the crimps on the headers, with no connector.. A fellow intern, which is a bit more sloppy with everything, was a bit nervous seeing that. He said that if he would do that, he would always short something out and kill it. Worked great for the few things I had to (re)configure over USB