Are Mac serial numbers sent to Apple?
To my knowledge, each and every time your Mac will send a serial number to Apple, you are prompted to explain this and why it will be sent as well as whatever information is needed.

You can see this in action from the System Information app:



When you click the "Check my service..." item you will see this alert:



Similar notifications are presented when the App Store app needs to verify your specific Mac is entitled to Lion during a restore. The Console app (in the Utilities folder) can be configured to send your diagnostic information which includes the serial number as well as other information about the hard drive, software and error logs to Apple.

You can also ask Apple if they treat this information as personally identifiable from their main privacy page. From what I can tell, they go to great lengths to treat this as other sensitive information and go out of the way to not lump it with your personal account other than when you do that by asking for service from AppleCare or registering your Mac.