That Nike+iPod thing always sounded nifty!
For fitness/nutrition tracking, I've used two programs: one a software program, the other a Web-based subscription system. I liked them both.
My favorite is the software, Nutribase. It's absolutely fabulous, and very flexible. You can add your own food items and recipes. You can track predefined workouts or input data from a heart rate monitor (HRM) or piece of gym equipment. There are several different packages of different prices, suitabe for the basic user to the professional nutritionist.
My boyfriend and I used Nutribase when we first started trying to eat healthfully and work out. I already knew a lot about calorie counts, but he didn't -- thanks to Nutribase he can estimate the calories of just about anything, and can immediately tell if a packaged food or a home-cooked meal is nutritious or not, the proper serving size or not, etc. He lost 15+ pounds with Nutribase, I think. He doesn't use it much now, prefering a more intuitive approach, and has lost another 15 pounds.
The online program I used was iShape.com. It was a lot like Nutribase, except scaled down and a litte more annoying with the custom food items. The best part about iShape is the community forum, where you get really quick and helpful responses from both users and iShape nutritionists and fitness experts on how to tweak your program, deal with plateaus, etc. It's a little more fun than Nutribase in that they have cool ways of tracking your overall fitness progress. You can view your total cardio time logged in the system as a map of how far (or how many times) across the United States your mileage accounts to (whether your cardio is running, walking, skiing, yoga, etc.). Your overall weights workouts can be viewed by total poundage. Like, your first workout, between all those reps of 5 lb weights, can add up to the weight of a VW bug! iShape.com is affiliated with Shape magazine.
No matter what you choose, though, here are a few tips:
The first two weeks of inputting food and fitness will be very time and labor intensive, because you have to put in all of your custom habits by scratch. After that, you'll probably be able to reuse most of what you put in before. Humans are creatures of habit.
Get a good food scale! I started with an "analog" one, and moved on to a digital one. Use whatever you prefer. And get lots of measuring cups and spoons, too. If you don't measure what you're inputting, your data will be completely wrong, and therefore completely useless.
A heart rate monitor isn't necessary, but it helps with accuracy a lot. Otherwise, you'll want to learn how to take your heart rate by hand, or use the rate of perceived exersion scale (RPE).
Hope that helps.
Have fun!