As you guessed it all depends. Sometimes it's not safe to swerve around an obstacle. If it's a long stretch of rough road, you can't hop over the whole thing. Typically if I can't avoid going over it, I'll "unweight" the bike by getting my butt off the saddle and using my arms and legs as a suspension. Actually, I feel more confident that I'll be able to maintain my balance in this position if the bike is getting knocked around a bit than if I'm seated.

If bad roads are a problem over a large portion of your commute, wider, lower pressure tires may help. If you're currently inflating your tires to the max pressure you could probably ease back 10 or 15 psi depending on how heavy you are and how much stuff you're bringing along with you.

If the roads are bad enough, a suspension may be warranted or maybe even taking a longer route to avoid the worst stuff.