I'm doing traditional illustration, so I actually do draw the word bubbles on the page. What I do is plan my panel so I know where it's going to go, write out the dialogue in all caps, draw the word bubble to fit around the words, and when I scan my art into Photoshop (I have an old copy), I erase the hand-written letters and type in my custom font in a size that roughly matches the size the hand-written letters were, so that the text fits the word bubble. (This ends up being about a size 16 or 18 font.)
Sometimes it works pretty well...
And sometimes it doesn't. Since I can't easily re-size the word bubbles, and sizing the font up or down too much looks weird, sometimes I have to either re-think the dialogue in a balloon... or just make it 'good enough'.
I've wondered about lettering/balloon programs before, and something intuitive that sort of formed the balloon around you words as you were typing them in would be great. Maybe something you could set to different types of balloons (thought, speech, SFX, etc). So yeah, sorry, I don't have a great answer for this either, I'm half-camping on here to see if anything comes up.