http://en.miui.com has some nice UX
http://paranoidandroid.co is nice if you want security
http://aokp.co has been around for years and stays cutting edge
CopperheadOS is what you want if you're concerned about security.
While I am happy Copperhead OS is around, it only supports a very limited set of Nexus devices. Back in the pre-Signal days Open Whisper Systems started their own work on an Android fork called WhisperCore. I'm curious if any of the features from WhisperCore ever made it into a new ROM, or if it was all quietly abandoned.
The former, FDE key separation, feature is gone and you'll need to either use adb or a 3rd party application [0] to achieve it.
It shouldn't be too hard to pull kernel patches from CopperheadOS and apply it to a clean AOSP tree for different devices -- this is obviously after they have done all the heavy lifting.