I used to have the same problem with stock seats. I use a Terry Liberator Pro on my road bike and my commuter bike. It has the cutout in the middle. My seat bones usually hurt for the first couple of rides until I break it in.
Stay away from seats with a lot of cushioning, it creates more friction which is DEFINATELY noticable when doing a century.
The Terry saddles are made by Sella Italia (a great bike saddle company). If your local lbs doesn't carry Terry, check out the sella italia trans-am or LDY models.
Good luck!