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Best practices for indie filmmakers, I think, include a range of resources that are available for as little cost as possible or completely free. I think bundling a whole lot of useful management resources that give your production an indie edge is an excellent way of trialling alternatives and it can also make the whole process more challenging and fun.
Managing projects is a difficult task and one that needs urgent attention when organising a structure consisting of multiple processes and people. There are a few free task managing tools that you can get your hands on to make independent production workflows more efficient, such as Task Coach and Rachota. These are Open Source tools freely available for public use. Some other interesting ones I have listed below:
1. Org Mode
The best way to trial these management tools is to just try them. There are other services that offer Team based management tools Online ... one I came across was Teamspace (free for students) and Teamwork Project Manager which has a 5mb storage cap on the free account. There are others with similar account plans, but make sure you test it out to see whether the free accounts cause too many restrictions for being able to orchestrate your team properly.