The Pectel (or similar) board was primarily introduced to protect a tuners work, by decrypting the software on the chip at run time - this was in an attempt to stop copying of chips..... they can also add useful features (depending on the board) such as anti-lag (for P8 EsCos ECU's) water injection etc.
Pectel is a company that made a mapping system for the Webber MArelli ECU's that our beloved Cossies use. The software creates an encrypted chip, the board decrypts it.
Stu did the 'perfect' description on a thread somewhere, which describes the ins and outs, but in a nutshell, what I've put above.
Not all tuners use them, some just use regular chips, and I think Stu @ MSD has his own protection system.