I use Family Historian to store all my genealogy data.
I find that I can keep track of individuals and associated events really easily. I can attach source information to each event/fact and make a note of where I found the information. It also produces reports and diagrams.
This was handy recently as my parents were going to a family party in Ireland so I took the opportunity to produce a quick report of my mother's side of the family for her to take with her. Before she went she had a few queries on some of the data and I was able to easily track back to the source. She was able to chat through details and add information to her copy of the report which she brought back for me to add.
It turns out that one of her cousins is interested in family history so hopefully we'll be able to help each other out in the future.
I also printed a copy of 1901 and 1911 census entries for her side of the family to show her brother - again I was able to do this direct from my software.
I also use Family Historian in my One Name Study and build families once I have enough proof.
What software do you use to organise your family history?