[GeoffR]

I've had my Glo for almost four years and never used anything but Linux with it in that time.

Calibre Has a Linux version. ADE is a Windows program but runs fine in WINE (I use ADE version 1.7.3). Alf's DRM-removal plugins work fine, I've bought hundreds of DRM ePubs from various retailers and the plugins have never failed to remove the DRM. Those are the only programs I have needed to use.

Edit: Also the program to patch the Kobo firmware works in Linux. Almost forgot that one.

(BTW if you have wi-fi then the Kobo desktop program is not needed at all. If you don't have wi-fi then you would need the desktop program to setup and sync the ereader. I don't know if it is possible to run that in Linux.)