The first is soooo simple: WalkJogRun let's you choose your starting point and then mouse over the route you took. You can cut across fields, hop up stairs and really calculate the actual route that you have taken, rather than some predetermined distance from point A to B. There's probably a great iPhone app that pulls this information in as you run, but since I don't have an iPhone I wouldn't know... (hint to the team that my birthday is coming up...).
I also really like Shape's Virtual Trainer. While it's time intensive and you have to stay on top of it every day, I love that it provides both exercise and nutrition tools. In fact it allows you to calculate your daily caloric input-output, which is really the most effective way to lose weight. The tool literally has every food/brand/portion/topping/flavor known to man; I can put in even the most obscure of meals and it calculates everything for me. I don't have to piece together the Cosi salad I had for lunch, it has that in there. I don't have to guesstimate how my Soy Latte differs from a regular Latte, it has that in there. I don't have to wonder if a NutriGrain bar is the same as the Strawberry Yogurt NutriGrain bars that I love, it has that in there. I think the thing I love the most about this tool is it's there when I want to use it and doesn't become useless when I don't. It doesn't rely on consistent use, nor does it harass me with emails and updates; it let's me do as I do and interact as I like. I heart it.