Yeah, I use AvaNetPrepare, which preps the hard drive with it installed in the Xbox. It will then populate your partitions with whatever you want it to over the network.
Aside from that, though, all the modern mod chips have built-in hard drive prep utilities.
For someone using a softmod, though, you'd probably be stuck with either the Linux disc or AvaNetPrepare. Between the two, though, AvaNetPrep is by far superior, IMO. Much easier, and no need to fool with opening up your PC's case, etc.