Lifehacker.com posted a list of the top things you might want to clean YOURSELF after you check in. Most are things guests touch a lot, but that housekeeping doesn't clean enough.
1. The TV remote. Everyone uses it.
2. The nightstand. Surfaces in general might not get wiped down enough.
3. The door handles. Another thing that every single guest touches.
4. The light switches.
5. The phone, if you plan to use it.
6. The handle on the minifridge.
7. The toilet handle. People don't wash their hands before they touch it, and it's the part of a toilet that gets overlooked.
8. The coffee maker. Run it through a cleaning cycle if it has one. If not, at least rinse the pot out. And if the mugs are ceramic or reusable, clean those too.