I used to prefer kobodl because it's standalone, which means you don't need other proprietary software like Adobe Digial Editions or Kindle for PC (that I can't use on Linux). However, I have since discoverd a way to do this with Calibre and 2 plugins:

Leseratte10/acsm-calibre-plugin - A plugin that can read Adobe Digital Editions files that Kobo web download produces.
noDRM/DeDRM_tools - The popular DRM removal plugin.
Now you can just download the .acm file from your book list on Kobo.com and load it into Calibre desktop!