Personally, when weighing bananas I weigh without the peel.  I've never weighed an apple before though, just logged it as 1 medium apple and figured that was close enough.

I usually pick small, medium, large..etc when eating those kinds of fruit.  If I were to weigh it, I'd enter the actual weight of what I ate. 

I believe the calories listed for those sizes take into account that you will not be eating the peel or core.   The reason I think this is one time I did weigh and eat a corn on the cob.  I weighed the cob when I finished the corn, subtracted it and it came very close to what CC listed as a corn on the cob weight.