I liked Fitday and used it for a while but then I got Fitday PC. Best $20 I've spent on software. I wondered how it was different too. Let see....
I can't remember the online version very well so I'll just say what I can about the PC version...
I can make anything a permanent "favorite" so I can quickly add it to my day
I can break down food, nutrients, etc. by meal
I've even put in a couple of recipes
I enter lots of custom foods...I just grab the package of what I'm eating and type it into the "Food Label" tab
I can set Weight goals and it will chart my progress.
It has tons of analysis that it will calculate
I know I'm not doing it justice with this explanation but hopefully some other users will pipe up and do a better job!
It's obvious that the programmer spends all his time working on making the PC version better while the online version will always just be "OK"....