About six month ago I bought my wife Sony PRS-505 eBook reader for her birthday. She uses it mainly to read Russian books. My home computer is dual boot Ubuntu/Windows machine, Ubuntu being the primary OS. When my wife downloads Cyrillic books they are in fb2 format and I prefer lrf for Sony Reader. So what I've been doing is sending downloaded books to my Dropbox and picking them up and converting once I am in Windows. Yes, I could have told my wife to use Windows when she downloads books, but I rather she uses Ubuntu, for obvious reasons.
Today I decided that this is enough and started looking for what is available on Ubuntu - I found Calibre. This is exactly what I was looking for! Calibre does exactly what I wanted - catalog my eBooks, convert between different formats and tons of other things that I have not tried yet. Open source wins again!