Having both (although my version of the BeBook is an EZ Reader - both are basically the Hanlin V3) here's my opinion. The Hanlin V3 (includes BeBook, ibook, Ez Reader to name the more familiar ones) is better when it comes to the hardware. The Cybook Gen3 is better on the software side. Personally, I mostly use the EZ Reader with OpenInkPot (OI) firmware loaded. The only real problem with OI is that it does not read any format that has DRM. On the other hand, I don't have any ebooks that have DRM. OI gives me mor flexibility for non-DRMed ebooks and has some very nice features that no other reader's firmware has (this includes Sony & Amazon)
That said, both the BeBook & the Cybook Gen3 will read .PRC ebooks with or without DRM. The Cybook has dictionary support which is often useful but probably not necessary. The BeBook firmware can read more different languages. Both are good buys, so I'd say go with the cheaper one and/or the one you can get better support with. Also if you can get a hands-on demo, I'd recommend that. All of mine were bought mail-order and I had some surprises (some good, some bad).
Of the 4 I have, I place them in the following order of how well I like them with the best first;
- Hanlin V3 (family) but with OI - best HW
- Cybook Gen3 - good SW
- Kindle 1 - Best SW but poor business model
- Sony PRS-500 - good HW but poor business model
Of course this is just my opinion.
EDIT:
DRM = Digital Rights Management
What it really means is that your ability to read the ebooks with DRM is restricted in some manner. With PRC, that manner is the units registered PID (Personnal ID). If you've been reading .PRCs on a PC you had to register the PC's PID when you bought the ebooks and they won't work on anything else, unless you register a new PID and re-download the book. Most places allow 3 or 4 PIDs to be registered.