fltplan.com > DUATS.
better organization of wx data. Only gives you pertinent info.
VERY accurate aircraft performance data
Shows what other aircraft previously filed as well as what the actual clearance was (makes planning a breeze)
EAPIS (not free, but very helpful and convenient!)
I really like how it gives you winds aloft for several different altitudes so you can choose the best one to fly.
The passenger briefing printout is a nice touch as well.
...thats all I can come with off the top of my head, but i am sure there are more things but I havent used DUATS in so long, I forgot what it was lacking!