Programs are the basic code that gives Transformers the instructions and motivation to do their jobs.
Types of programs
Combat programs are progams which allow Transformers to adequately perform in combat situations. Bumblebee maintains that as a repair-bot, he isn't programed for combat. Fortunately, that doesn't stop him.
Humility programs are the basic programs that allow Transformers to feel humility, shame, and a sense of place. Ironhide believes that humility programming is best installed via fists. It's highly unlikely that Optimus Prime would agree with that.
Personality programs are the programs which set Transformers apart from regular machines. Only Vector Sigma can grant true personality programs to robots.
Predictive programs are programs which allow Transformers to predict where shots are going to be fired and where an enemy is likely to strike in combat. Very advanced, they make hitting a Transformer in open space very hard. But not impossible.
Timing programs are the programming that modulates the speed at which Transformers speak or react. Sandstorm once asked if there was something wrong with Blurr's timing program, but Kup says that this is the way Blurr was made...frightening.