They're a pretty cool way to show narrative ques, especially in horror.
For myself, I use them to show:
A) A character isn't human or is no longer human.
B) The information provided has changed the situation/mood of the story.
C) Narrative repetition (such as repeating previous info/dialogue with different meaning).
D) Dramatic irony and let the readers in on hidden information.
Since I work mostly in horror, different colored speech bubbles have really worked in my favor, especially if I'm going for a sudden shift in the mood or want to introduce some horrid scenes. Though I can see how it might feel out of place in, say, a romantic comic or comedy (even then -- could still work depending on how it's implemented).
Like most comic techniques, it's all about practice. Nothing a bit of experimenting can't fix.