Applications :: Note Taking And Tagging Software

I am writing a doctorate, mostly based on archival sources (being a historian), and recently noticed how the inefficiency of my notetaking seems to have at least some degree of negative impact on my research. In previous years, writing shorter papers and articles, I mostly replicated the structure of sources in my notes - thus documents were described under archival units etc. Why perhaps not efficient, it was nonetheless perfectly acceptable. However, this time, having read a few thousand pages and noted down a few hundred of documents and sources, I find the old system completely inadequate - since the archival structure is itself semi-formal and the division not perfect, looking for information within my notes is getting almost as tedious as reading the sources itself.

I would therefore love to get a decent application that would allow me to take notes (mostly text, but graphics, pdfs, links etc would be appreciated as well), and tag them accordingly. This would allow for easy access to information. A welcome feature would be syncing between my imac and macbook - right now I am forced to only use the latter, as updating the ever changing 'academia' folder manually every single time got old fast. So, would you have any suggestions? I realise no freeware will do this and I'm willing to pay good money for the described feature set (provided a single licence would allow me to use it on multiple computers). I am also interested in good writing software, as Pages will only get you so far once the document grows over a certain number of chapters, pages and footnotes, but note taking takes priority.