It basically means "what do you think of that!?" in a very smug manner. In the Good Will Hunting scene, Damon takes the expression and stretches it out, asking the other guy "Do you like apples?" (which sounds like a normal question, albeit a strange time to ask) so he can really rub it in when he shows off the girl's number.

The bar scene? Do a google search for the English subtitles. You can download the subtitles file and then find the exact dialog. If you can't find it, let me know and I will post it here.

...them apples = ...those apples It is slang.