I used Eagle 5 then switched to Eagle 6. Fortunately, I’ve been able to convert my previous Eagle 5 projects to Eagle 6, but there have been many quirks, such as polygon copper planes being offset, pins in my libraries being re-oriented, airwires that refuse to be routed unless they are deleted and added back in, etc. Nothing that isn’t fixable, but it was a pain to manually go through them and fix.
In my opinion, Eagle 6 still feels like a Beta product. If you have the luxury of staying with Eagle 5 until Eagle 6 matures a bit more, I’d recommend it, especially since the gains in Eagle 6 are minimal. For example, in Eagle 6 my entire library of custom parts became corrupted, because somehow all the symbols somehow got renamed to “PNP” in the XML file, and I could no longer open the library in Eagle. Fortunately, I reverted to one of the auto-generated backups which was made before all my library symbols got magically renamed to the same name. Certain settings in the CAM Processor also cause Eagle 6 to crash a lot, even though Eagle 5 had no problems with them.