First off, I'm running ubuntu jaunty beta and I have to say, these programs do INDEED work under wine 1.0.1
I've used wiiscrubber, wiibrickblocker, and freethewads under wine cmd.exe
the original wbfs tool is an original linux tool that's been ported (with some broken functionality at that) and is more reliable to use than the windows equivalents
if you're not happy with that, install a virtual machine such as sun xvm virtualbox or one of hundreds of others out there
run the program natively on the isos and then copy them using wbfs from linux (I've yet to have a single error/problem with the linux wbfs tool while I hear constant bitching elsewhere about the windows one ruining partitions--but that might just be user error)