How do I make my external Thunderbolt 27" display's brightness match my iMac's brightness?
The best, albeit somewhat expensive, way is to use a spectrophotometer to create accurate color profiles for each of the two monitors. Short of that, you can use the built-in calibration software, accessed using the Monitors control panel, to create the profiles by eye.

According to Apple's documentation on Calibrating displays with built-in ambient light sensing you should disable the automatic feature while creating the color profile. They claim you can then re-enable it, but for color critical work I would consider leaving this function disabled and controling the environmental light instead.

Unfortunately, there are reports of Mac OS X 10.7 not working properly using different profiles for two monitors. You may have to manually (or use an Automator script to) assign the correct profile to each monitor after every restart.