Atleast my experience is that all of WCG's sub-projects gives roughly the same credit/hour as the other sub-projects, atleast under windows, but some does claim linux has an advantage for a couple of them while windows has an advantage for atleast one of them. Still, my recommendation is to run whatever sub-project-mix you want yourself.
But, Clean Energy Project 2, CEP2, does need some special considerations. For one thing CEP2 has fairly large uploads, so if you've got any form of monthly transfer-limits or something it's probably not for you. Another thing is that checkpoints in CEP2 is few and far between, if not mis-remembers have seen over 8 hours between checkpoints on an i7-920, so any computer that's often re-booted or something should not run CEP2.
Also, CEP2 is very demanding on the disk-system. The size on disk isn't the problem, even it's around 700 MB per wu. It's the huge amount of files and that even there's a long time between checkpoints CEP2 is nearly continuously writing to disk that is the problem. This means that if you tries to run "too many" CEP2 at once, there's a very good chance you'll hit the dreaded "No heartbeat for 30 seconds", something that means that ALL WU'S in memory will be re-started from last checkpoint. With the multi-hours between checkpoints even a single such re-start will lose many hours of crunching. :sad:
So, if your BOINC data-directory isn't running-off a SSD, my recommendation is to limit CEP2 to maybe 4 wu's at once, something that is configurable among the WCG-preferences on the web-page.
BTW, the default CEP2 is to limit to a single wu at once, so always remember to increase this a little if you want to run multiple CEP2-wu's.