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Apple Issues Warning on iPhone Unlocking [Updated]
Apple has discovered that many of the unauthorized iPhone unlocking programs available on the Internet cause irreparable damage to the iPhone's software, which will likely result in the modified iPhone becoming permanently inoperable when a future Apple-supplied iPhone software update is installed.
Apple plans to release the next iPhone software update later this week which will include the iTunes Wi-Fi Music Store.
It appears the statement only refers to SIM Unlocking your iPhone to allow it to use networks outside of AT&T. It would appear that 3rd party hacks (Ringtones, Applications) would not cause the same problems.
One forum user indicates it is possible to reverse the SIM Unlock by reflashing the firmware but must be done manually at this time.
Update: A rough guide to relock your iPhone, ahead of the software update.