What are the best ways to organize one's research workflow when it comes to tracing articles, tutorials, web pages and videos?

I have a good memory, but some of the fields I'm working in (NLP, Semantic Web, Information Visualization, Machine Learning) are quickly expanding.

While I do have a good method of keeping track of good research (I only follow the best researchers and research groups on Twitter, Scholar, conferences, journals, etc), sometimes perhaps it's better to save all the interesting papers, add notes to them and put them in context and relationships with other papers (if a paper frequently cites another paper and is a sequel to that paper, perhaps it's better to read those 2 papers together, for example). Essentially the things I want to do are these:

• keep records of the workshops, classes or tutorials I attended, but also video recordings of presentations I have never seen in real life


• annotate PDFs, extract metadata from them and generate bibtex bibliographies


• keep tutorials in pdf + video format synced (where possible)


• keep everything in context - organized in folders, tagged,
  
  cross-referenced if possible (if an article is cited in a paper and I already have it in my library, I want to be able to access it fast)


• I want to be able to search about various keywords/tags regardless of the location where the actual files are stored and OS.

I noticed most of these things are doable in the Apple ecosystem (iTunes, iBooks, etc), but not really on Windows and Linux. Does anyone has any idea about how to do this in Linux and Windows? I happen to absolutely need to use both operating systems (still have some work with SQL Server, Excel, etc), but most of my development work is in Linux (coding in Java, Python, JavaScript and others, but also writing papers in LaTeX).

I would preferably only sync a huge zotero (or similar) folder using Dropbox, and papers/tutorials should be in folders related to their research field, but also tagged so that I can find them regardless of the folder.