I haven't look at myfitnesspal (I use my own spreadsheet to track calories), but most sites/programs that compute calories for exercise you shouldn't trust. If they're accurate at all, they still probably use total calories burned, whereas you want to record net calories burned (calories burned - basal metabolic rate, the calories you would have burned anyway sitting on your ass).

Fortunately for most of us it's pretty simple; all we have to do is credit calories per mile run. To determine that, see 

How Many Calories Are You Really Burning?

Myfitnesspal does let you log exercise - its painful with lifting so I just enter the running - it goes in 0.5 MPH increments from what I've seen and it does show you burn more at a faster pace and as your weight drop you burn a little less at the same pace.  That all makes sense and goes along with what I know about calorie burning.  Whether its exact or not I don't know but seems to be close enough.  I agree some people will burn more than others just sitting - I know I do.

Yes ice cream is a particular weakness along with Little Debbies.  I'm trying to save $ so I switched a lot of Little Debbies to Walmart brand.  It tastes OK but not quite as good so they haven't disappeared so fast.  I've only hit the pint of Ben&Jerry's once since this diet but I'll still pile up a bowl of 3 or 4 scoops every week or two...just not every night along with other snacks!

npaden - the slower paced run is probably close to the middle of the 137 and 65.

kmays - wow, I've never finished a day in the negatives!  The closest I've gotten was a day of a 10-miler when I slept in and skipped breakfast.  I was under 1,000.

Myfitnesspal does let you log exercise - its painful with lifting so I just enter the running - it goes in 0.5 MPH increments from what I've seen and it does show you burn more at a faster pace and as your weight drop you burn a little less at the same pace. 

That makes it more complicated than it needs to be. What, you choose pace and how long you ran? That's recording (the wrong) two variables, when one will do. Just count calories per mile burned. It's almost independent of pace.

Well calorie counting works in some respect but there are a couple
of issues with that. Not all calories are the same - there is a 
difference in terms of the body responding to either high- and low- 
quality calories in terms of hormone release. Hormones play an important
part in weight and especially fat loss. High quality calories contain
plenty of nutrients (vitamins, minerals, amino acids...) and they
are less likely to be converted to body fat. The whole calorie in
calorie out rule isn't really true and far too simplistic.

I'm not getting hung up too much on calories anymore but focus on
the quality of food, remove sugar as much as possible, include good
fats and eat mainly protein and carbohydrates from vegetables.

Calorie counting creates an awareness but if you want to take it
further or get stuck with your weight loss I suggest to look
into this closer.

The whole calorie in
calorie out rule isn't really true and far too simplistic.

Technically true, but not really relevant if you have a good calorie-counting methodology. The question is not whether all calories are exactly the same, but rather what is the effect of operating as if they were?

And the good news is, calories counting -- without any regard at all for where the calories come from -- works just fine, as long as you actually do it, and as long as you adjust your calorie budget based on feedback from actual weight data. The magic is all in the feedback. You have to (1) plot a moving average, rather than just looking at daily weight, and (2) over time, observe the trend of this average, in lbs lost per week. Almost  by definition, this plan is guaranteed to result in losing weight at whatever rate you are able to sustain in terms of calorie deficit. Of course, a given calorie deficit may be easier or harder to maintain depending on what kind of calories you are eating.

Getting lost in the details of physiological responses to different calorie sources (many of which are poorly understood, active areas of research) can make a perfectly tractable task intractable. I was stuck with this mindset for years, unable to do anything about my weight because I didn't understand all the variables. Then I read the Hacker's Diet, a light went off, I lost 50 pounds, kept it off, and now I run sub-3 marathons and hundred milers.

I use the app too, I tend to get in a snacking habit and gradually increase portion sizes, so this helps me keep track.

My issue is balancing calories in vs calories out, I get that it's a basic formula, but in my efforts to reduce calories I find that I can't finish my runs.  Perhaps I'm imagining it, but it seems to catch up with me on day 3.