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.