Well I'm in the same boat as you. I'm still looking through cameras for myself, but I've been looking at these 2 pretty hard.
The thing with the Canon Vixia HF S10 is that it's got an easier design to control. All the external buttons are easier to find and use. It is also completely digital making it (in my opinion) more "user friendly," but i have met people who like tapes for archival purposes. The down side is that it looks like a normal handycam which doesn't seem all that bad, but if you are working with an outside source they'll usually tend to think bigger is better.
The Sony HDR-FX 1000 has that professional look to it which will impress clients. Although what you get with professional look you sacrifice controlability. The joystick for it is at the bottom of the camera and if you have large fingers you'll have a hard time using it as your finger will usually slip off and there is no remote for it. This will make the Sony much harder to use in run&guns and on the move movies. This all sounds like a big put off because well it is, but Sony made this camera better in a key area. The FX 1000's low light capabilities are much better so if you shoot in low light this might be a good one to look at.