We used to file them manually in the old days! It's not the difficult, assuming you have an up to date set of charts (as every operator does!)
We have been using Jeppesen JAS for Windows for the best part of ten years. About two years ago we started to look at PPS as it seemed a far more user friendly system and we didn't have to pay for each flight plan we ran (which we do with Jepps). However, since the recent advent of <a href="http://www.jetplan.com," target="_blank">www.jetplan.com,</a> Jeppesen's internet portal, the decision has not been easy.
However, this was a topic about making flight planning cheaper. I've not used them, but what about the FlightStar that Jepps make - I've no idea about price though.
Sabre Aviator's post is quite true, although I've yet to find a system that is 100% correct. Even 75% would be a bonus!
The other alternative is to get the CFMU access (any commercial operator can get it), and then use the route database function to get your route. Then just write your own fuel plan. Or keep a record of your standard routes and then just construct a new flight plan on a new route. Should take about 20 mins per route, unless things go really badly! You can also get your handling agent to file it, any self respecting one will give you a decent route...
Hope my ramblings help!