I was always kind of irked by the seemingly arbitrary application of hole dims to the hole wizard tool myself. I generally apply the dimensions that I want/need manually at the time I employ the wizard.
To provide another answer your question, I know that somewhere in the SW installation directory are a series of MSAccess database files (*.mdb) that can be modified according to your preferences. The caveat is that you'll want to backup the original because I believe that I've read here in the forum where sometimes these tables can get screwed up and mess with the SW installation.
Oh BTW, I believe that this suggestion is only applicable to SW03 and prior. SW04 I think does away with these and allows the user to interface and create favorites within SW itself (as was suggested already) but I'm not 100% certain of this.
Good luck,
Chris Gervais
Sr. Mechanical Designer
Lytron Corp.