Thought I'd start a general discussion on the subject. Feel free to share your thoughts or any tips on how to avoid it!
So who here's bothered by it? haha 
I've noticed a lot of series kinda suffer from this (popular and otherwise), however I'll give a pass to gag-a-days/comedy, "chibi" styles and styles like Adventure Time where they're not even trying to distinguish humanoid faces really (there is most certainly a charm to styles where a face is just a mouth and dots for eyes). Here I'm talking about story driven material where character distinction is important. I know characters can be distinguished by their hair, skin tone, and outfits, but I personally like to be able to tell people apart even when they're stripped down, bald, and just drawn in outlines. I also find it disappointing when you know the artist is definitely capable, they are technically sound and can draw some pretty awesome things, but all their people look the same. It's hard to connect with the characters unless they're written very well, at least in my experience. -_-
I know it can be hard to break out of your usual style, but you can't improve unless you try new things I say.
I'll admit, sometimes I myself worry if I draw a person and they look too similar to another character I've already established.