Most of the startups that are making money are the ones you've never heard of. This is a pointless exercise...however, here are some that I believe are making money that you may have heard of (happy to be corrected as I don't know for sure that they're all making money):
1. GitHub 2. eBuddy 3. Dogster 4. StyleDiary 5. ThisNext 6. Kaboodle 7. Stateless Systems 8. RedBubble 9. Wufoo 10. NationMaster