Pros: With the right tuner/cai combo and program, gains can register 20-25 hp at the wheels which translate to only about $20 per rwhp. That's cheap when you consider most mods can cost twice that per rwhp.
Cons: None unless you are under warranty and a problem can be traced to a modification of the PCM strategy code. Rare, but I've heard of instances where that has occurred.
Generally speaking, the hp/torque increase from stock and fun factor that comes with it is worth the cost. IMHO, if you can afford it - do it - but make sure you find a reliable programmer.
2006 GT Redfire 5 Spd Manual. Saleen S/C. Custom Diablo tune by Adam @ ST Motorsports, San Bernardino, CA.