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Holding to-do's and project information in one application is difficult. I've tried a lot of applications and (obviously) use OmniFocus for my GTD stuff. I have settled on DEVONthink to store project information, and everything else in my life. I'm somewhat of a rookie with DEVONthink and have found the learning curve somewhat steep. However, the other PIM applications don't match up to the power of DEVONthink (although I do like Eagle Filer a lot).