My system is pretty simple now
I have eReader and Mobipocket format books I've bought in the past, but if it's only available commercially now, I buy LIT format and use convertlit to read them with µbook. _All_ my ebook/novel reading is done in µbook now, though I keep registered versions of eReader, Mobipocket and iSilo installed "just in case" for my older books. Almost all my ebooks are now in zipped HTML or RTF format, so I will always be able to read them in the future.
Any news or online content is read with iSilo/iSiloX of course, which is still the master of presenting HTML/online content in a mobile friendly format.