I have both the Q3 and Q3HD. (And the H4. I like Zoom products, can you tell?
) I do not hear any difference in the audio quality between Q3 and Q3HD, but the improvement in picture quality is (not surprisingly) substantial in the Q3HD.
I'm a big fan of the Zoom products for their all-around ease of use and versatility, but then again, I'm not an audiophile and do not consider myself a computer or technology whiz. And while it may not be "hard" to use computer software to combine audio and video, I find it to be a bit of a pain in the butt. Sometimes a big pain in the butt.
So, I think it will depend on how much a priority you place on convenience and ease of use. If you want to get the best possible sound, follow Ron's advice (and, heck, go whole hog and get separate microphones, a mixer, etc. etc...). For YouTube purposes, where everything is compressed anyway, I take a satisficing approach, and I use the Q3HD. But I use the H4 (which gives me slightly better sound than either of the Q3 units) and record in .wav format for making my annual compilation CDs.