Are there any tools for organising literature with tags?
I use Qiqqa to manage my PDFs when writing research papers. It allows you to highlight text or add notes to the PDFs. You can then tag the notes, and run "reports" which essentially will pull all of the tagged sections from all of the PDFs in your library into a single paper (similar to the Word document you mentioned) so you don't have to do that manually. It will show the original snippet from the paper, any notes you've made regarding that snippet, and the citation for the paper. There's also a neat brainstorm function that will let you visualize papers, tags, or notes and move them around/link them together; I use that to organize papers sometimes. 

There is a free version which will let you try out some features, and an affordable pay version that has more enhanced options. There are some helpful how to videos on Youtube that provide a nice sense of functionality and may help you decide if it's the tool you're looking for. I've been using it since I started grad school and it's been tremendously helpful in organizing my academic writing.

http://www.qiqqa.com/67642