I'm still struggling with this. What I wouldn't give to have the money for a bodybugg (I think that's the name?) that I could wear and know exactly how many calories I'm burning. But alas, I am a poor college student, and even $30 for a basic heart rate monitor is a chunk of change for me to spend on a gadget.
The way I've been determining the calories I've been burning is through caloriecount.com. It has ziiiillions of activities to choose from, I type in my minutes, it knows my height/weight/frame, and it records how many calories I supposedly burned. Also, on cardio machines at the gym, I always plug my weight in 15lbs lower than my actual weight. So right now, I'm 142, when the treadmill asks my weight, I say 127lbs. Hopefully this does some to make up for the gross overestimation of burned calories on those machines. Generally, that number is very close to the number that caloriecount.com estimates. For example, the treadmill tells me I've burned 150 calories after 15:40min of running at 5.2mph. When I plug "running - 5.2mph, 15min" into caloriecount, it tells me I burned 147 calories.
I also purposefully record less exercise than I actually do. So, I might run 27min, but record it as 25min. Or I might walk for 30min on an incline, but record it as level ground. And of course, I never record normal daily movement as exercise. Walking around Walmart for 40 min or carrying 10lbs of textbooks uphill to class must burn some calories, but I do not record them.
So, I'm proactively trying to avoid calorie burn overestimation, but I'm always paranoid that I'm not doing enough. What if I'm assuming that I've burned 500 calories, and adjust my calorie intake for the day around that number, when I'm really only burning 350? Thoughts like that concern me.