I don't typically worry about bye weeks too much. However, one thing I like to do which has proven very useful is this:
During the draft, I monitor my schedule and the bye weeks of my opponents (using DD of course!) For example, let's say I'm playing TEAM A in week 9, and I notice that in the first four rounds he has drafted two players that are both on bye week 9. If I'm trying to decide between two or three players who I all have ranked equally when it is my turn to pick, I will take the one that is on bye week 9. Why? I already know I'll have an advantage that week, so taking a player on bye that week won't hurt me as much.
This actually just happened to me in a draft I am in. The team I am scheduled to play week 9 drafted Steven Jackson and Ronnie Brown with his first two picks. His top two running backs are both on bye the week I play him! When it was my turn to pick I wanted a WR from a closely grouped tier of available players, and I targeted Plaxico Burress (who is also on bye week 9). So just as normal, one of my starting WR's will be out for a week, but I specifically targeted it to be week 9 when it won't hurt too much to be missing one of my starting WR's!
LOL, unfortunately Burress was selected two picks before me, so it didn't work out that time, but I have pulled it off in previous years to great effect - I think a smart drafter should always look for such opportunities to maximize the value of every pick.