iPhone OS 3.0 has provided lots of features that were missing in earlier version of iPhone OS. There is still a missing feature for deleting individuate call record. I have used weTool to perform this action in past. It seems that weTool is no longer available for iPhone OS 3 onward.
CallClear is a replacement for weTool up to some extent. It allows you to delete individual call record one by one from call history. CallClear is available on Cydia.

Related posts:

1. weTool: A must utility for iPhone
2. Manage messages in iPhone (Forward, delete individual message)
3. Speech recognition for the iPhone
4. Call History Patch
5. iVideoCamera – Record video on iPhone 2G & 3G officially