*. Searching and finding them easily.
*. Keep them in categories (like in libraries :P).
*. Manage thousands of e-book collections easily (as said above you can "sort" them by the: Author, covers, Titles, etc).
*. Automatically fetching e-book meta info (which automatically imports information such as author/year, etc).
*. Sync between different devices (Linux Laptop to iPhone/Amazon Kindle, etc).
*. Convert them into different formats.
*. Find e-book sellers online... seriously, do you need more than that :).
If you want all those above mentioned features and many more of minor other features, then I urge you to try the awesome Calibre e-book manager!. If you use Ubuntu 11.04 Natty Narwhal then you can easily install Calibre by using a PPA channel. To do that, as usual, open your Terminal and issue the below command.
sudo apt-add-repository ppa:n-muench/calibre
sudo apt-get update
sudo apt-get install calibre