Nosferatu, A Symphony Of Terror(1922)
Not so much the Granddaddy of indie films, as the mad Great uncle, when F.W. Murnau decided he wanted to adapt Bram Stoker's Dracula, he didn't let legal threats stop him - he just changed the names and made a few tweaks. Murnau's ingenuity (and a court order) gets him in here, but Nosferatu is also one of the best silent films ever made, and one of the creepiest, sound or no. It contributed to making German Expressionism an entire chapter in the cinema history books, and is among the most homaged, pastiched, and parodied films ever made - so indie they had to make an indie film about it.
Roger And Me(1989)
Before the Oscar-winning Bowling for Columbine and the headline grabbing Fahrenheit 9/11, Michael Moore made a documentary about the closure of the automobile plant in his hometown of Flint, Michigan and the economic devastation that followed it, and it made his reputation. All Moore's polemic skills are apparent here - there's the same sly cross-cutting, the persistent hounding of people determined not to talk to him, and interviews with the sort of 'ordinary' everyday loons that only exist in small American towns. Arguably better than its successors - Moore punctures pomposity in others without appearing pompous himself - this is rabble-rousing stuff.