In Lisa Jhung's Runner's World blog (Running For Two - Great read - you should check it out), she mentions the apparel she's found helpful for running while pregnant.
I haven't tried any of the stuff she has although it sounds interesting. Right now I am primarily wearing Nike maternity shorts with my some of my husband's technical tees. (Shh- don't tell him as he will freak that I am stretching them out). I have a bunch of Nike maternity long tanks but they are too big to wear right now.
Unfortunately Nike stopped selling their maternity line a few years ago. However, I have been able to get a bunch of stuff off of eBay. It's Nike quality which I really dig. It seems like the active wear you get at Motherhood Maternity or Target is designed for the mommy-to-be whose fitness regime consists of yoga and a few strolls around the block. If I am going to be running or spinning for an hour I need to look cute AND have moisture wicking!
The only other wardrobe change I have made is to wear two sports bras. I'm not large chested but have grown some since becoming pregnant. The double protection makes me feel much more comfortable.