In the past, I've used MobileLog on my iPhone 3GS and it worked great. I just upgraded to the iPhone 4, and MobileLog crashes the Phone app if I set it to replace the default Recent Call Log (like I did on the 3GS).
I just tried CallLogPro but, amazingly, there is no option to let it replace the default Recent Call Log (they say it's a planned update).
Is there any other program out there that will delete individual calls in the Call Log (why this isn't a stock option like every other phone out there is ridiculous), and allow itself to replace the default call log?
I'm going to assume you're already Jailbroken. If so, you can download an app in Cydia called "Call Clear". This will allow you to delete any calls that you don't want in your call log.