Both the Engine Control Unit and the Transmission Control Unit can be programmed by aftermarket software to achieve increased power.
The TCU is the most direct of the two. Currently MTM and Viper UK offer an over the counter TCU tune. This is usually flashed to a new chip module, then soldered into the main board. Be careful if you're doing the soldering as I've seen a TCU board go bad costing $500 for a new one. These tunes will generally tighten up the shift time from one gear to another; allow higher RPM points for shifting when in Drive Mode; and removal of the kickdown switch function when in Tiptronic Mode. The quicker shifting reduces wear on the clutch packs, and gives a slightly sportier feel. Sport Mode from the factory has very high shift points and quick shift timing already in place, but is a bit jumpy and aggressive for daily driving.
The ECU tuning is done by at least 10 companies in the U.S. and abroad. Some of the primary off the shelf names are APR, Eurocharged, Viper, and Revo. Smaller companies such as EPL and AMD will also tune for those who have switched to a 6-speed manual transmission. The tunes generally increase boost, timing, and fueling. The end result being roughly 60 horsepower and 100 torque more than stock; a significant increase compared to the 450hp/425tq from the factory tune. This extra power puts more strain on the car overall, namely the transmission, but if driven with care it has been holding up well in most applications. Driving style makes a big difference in wear/tear on the transmission and other parts.
An important upgrade to go along with the extra power is certainly the MTM, AMD, 034 Motorsports, or Viper TCU tune; as this tightens up the time between shifts, reducing wear on the clutch packs. Many of those who have had the original automatic transmission fail on them have now upgraded to a rebuild trans. These rebuilt and beefed up transmissions tend to have increased Valve Body pressure to tighten shifts even more, along with stronger internals and upgraded clutch packs. Unfortunately due to the design of the transmission it can only be made so strong, and remains the primary weak point of the car.