In order to keep track of the different branches of my family tree, I use the free (and private) Family Echo family tree maker. This allows me to compile basic information for each member of my family, including names, dates and relationships in a pedigree chart diagram. I also use the Ahnentafel numbering system to assign a unique number to every individual.

The information I collect is logged into Evernote. I create a notebook for each family branch and an individual note for each person. Within these notes, I make sure to match each piece of information to the source that provided it. I also have a separate notebook where I enter translated and transcripted documents into individual notes for easy searching. I find Evernote a fantastic resource for organizing genealogy notes.