I like them both, they're pretty much equal imho. I used Apex initially for AOKP on my Razr, but soon switched to Nova because it had a few more features earlier on. Switched back to try Apex when Nova was having some issues, and Apex now has the same features. From what I hear Nova is once again stable and smooth, but I have my Apex pretty well set up and simply haven't bothered to set it all up again on Nova.
Honestly I find it very difficult to tell the difference anymore. If you want to compare the two for yourself, just set them both up the same and keep your launcher default clear for a few days. You'll find pretty soon which one you end up using more often, and go with that. But you can't lose either way, imho.