The above AFPEX site is one I use. A good system with lots of features, but downloads a 5MG java application every time you start it, making it virtually unusable when mobile on GPRS/3G.
Homebriefing is another. Not free but very good. I use this too - for when on the move. For Euro 37 they will do 10 flight plans, after which you have to prepay some more. They do unlimited flight plans if one end is in Austria or Switzerland.
As for sites which will do flight plans for anywhere to anywhere, that is all that is known.
There are other sites but they are limited to flight plans starting or ending in a particular country.