I would definitely recommend Calibre for the book sorting and archiving features alone. You can also use it to view epub files. I'd experiment around with the conversions it offers and see which formats you like best. I do much reading on a netbook, so I like to have formats that I can view in programs with a true fullscreen mode without any menu bars, so I might choose pdf or rtf. Sadly, as far as I can see, Calibre doesn't have such a mode in its internal viewer yet.

I'd recommend keeping the original files (Calibre does allow you to keep multiple formats of the same book in the archive). When you get a reader, you can then convert things to whatever format is recommended for that reader; Calibre supports a number of devices.