Remus Lupin was the mastermind of all the pranks the Marauders did. Who would suspect mild mannered Remus to come up with the most insane prank ideas? No one that's who.
Peter was the scout. He always had an easier time fading in the background, gathering information about the spot where they would place the prank, the people they targeted (years later when he became a spy for the Dark Lord he would consider this to be his training, after all who would think Peter Pettigrew to be capable of being a spy?) It got even easier after they became Animagi because Hogwarts was full of rats. He became so accustomed to being ignored and glossed over that he sometimes wondered if anyone even knew who he really was (sometimes he forgot too).
James and Sirius were the power behind the prank, James with transfiguration and Sirius with charms (he could alter spells like nobody's business with a bit of time to work out the kinks). And James was always a powerhouse, his transfigurations lasted longer, his curses inflicting more damage than normal (his cutting curse was capable of decapitation if he wasn't careful).
They also came up with the best cover stories or provide diversions when they needed to distract the teachers. Because it was always James and Sirius the teachers first mention when they talk about the Marauders (and they thought they had them pegged but they forgot James' mother was a Black and Sirius, though a Gryffindor, was a Slytherin at his core)
Remus was the brain behind everything. He chose their targets and decided when and how they would strike. James and Sirius were divas, they wanted the attention, they wanted the school to know they were behind the prank but when Remus was behind them no one could figure who did it (one time they managed to convince the teachers and the school that a group of Slytherins were behind the prank and did it so masterfully that even the Slytherins were convinced they made the prank and then forgot about it).
When they needed potions for the prank he was the one who brewed them in a forgotten classroom, who spent hours inventing new ones or altering others for their purposes (it took him a lot of trial and error, and explosions, before he became good at it and in their seventh year, when Lily started dating James, she would join and help)
His pranks could be compared to karma (if you believed in such a thing), in contrast to the attacks on Slytherins that James and Sirius did. Remus believed in justice and fairness above all so every prank he was behind would be just what you deserved. He changed tactics in seventh year when the war finally reared its ugly face, and while they still weren't cruel and overly embarrassing for the target, they gained an edge that they didn't have before (they don't talk about the "war" that took place in February between them and the Slytherins that needed the interference of Dumbledore to be stopped)
McGonagall made him Prefect in the hope that he could rein in James and Sirius but she didn't realize that it was usually James and Sirius who needed to rein in Remus. Though it seemed that Dumbledore knew because come seventh year James became Head Boy (Remus asked him when he came to teach DADA if he knew but all he got was a smile and twinkling eyes).
Years later when Teddy Lupin comes to Hogwarts and is sorted into Hufflepuff McGonagall thinks that she dodged a bullet until one morning the Great Hall is filled with kittens and she realizes with dawning horror that she made a great mistake (Teddy, after all, is the son of a Marauder and a woman who, for one week, came to class with the face of the professor who was teaching the class, and the less said about his godfather the better).
When James Sirius is born she puts her head in her hands and decides that she will retire the day he gets his letter (she doesn't).