Quote From Hugh:
Look at endnote, I think that may be what you are looking for. NVivo can be temperamental and it's not organised well.
I also used Mendeley to organise files and notes, and word docs too.
I do use Endnote but it is very much a reference management software. I am wanting something that allows me to make summaries of the journal articles I read, connect these summaries together, store whatever lab work and procedures I have done, make mind-maps etc. As my PhD is a part-time PhD, the project will at least take 4-5 years. So, as much as I prefer doing things on paper, it is not going to be practical to maintain everything in hard-copy format over many years.