All you need to do is setup a Windows (XP, for best) and the rest is a simple as setting your virtual xp to hibernation. Whenever you want to put a rom on your Flashboy it is a task of seconds, instead of rebooting you machine, switch to windows, install a game and than reboot to get back on the light sight of things, namely Mac OS.
I setup a shared folder that is mounted on the windows side. Putting roms in there (links doesn’t work) makes the file transfer between mac and xp very easy and confortable. Here’s a tutorial on how to set it up: http://showmedo.com/videotutorials/video?name=3650000&fromSeriesID=365
Note that you will have to choose the USB Port where FlashBoy is connected in the Virtual Box settings and unplug and replug it when XP has booted.
I haven’t tried Fusion nor Parallels. Both feature a good coherend mode where windows runs transparently on you mac desktop. I believe it is eating up way too much resources (RAM, CPU) for such a small task, besides that both cost a couple of bucks. Virtual Box is free, though.