+1 to calibre for managing your books. And
https://apprenticealf.wordpress.com for DeDRMing them. (That isn't so much open-source as it is broken open with a crowbar.
)
As for hardware, there are no E-Ink ereaders which are truly open-source, though some are more open than others. You probably want one that can be jailbroken, though -- at the least.
Maybe one of the more open Android phones. There are some open-source ereader apps out there.
If you want usability over ideology, ask yourself which features you need, and look for a device that has those features.