New answers tagged note-taking
I would suggest to use TagSpaces. It is open source, and allows editing and tagging of multiple file types. It also enables different views like you mentioned. The best thing about it in my opinion is that you can use it with any cloud storage you like.
A possible alternative to Trello if you want an offline option would be Wikidpad. It's quite barebones, since it's technically designed for building up a knowledgebase, but you can create pages for your things, then link to those pages from pretty much anywhere else in your file you want.
From your requirements above, it would seem that Trello may be a good solution to your preferred organization system. A single Trello 'board' contains a system of 'lists' which can contain unlimited 'cards'. Each card can contain a variety of content including tags, links, files, etc. And Trello can very easily be setup for GTD use.
If i understand you correctly you're looking for a system that automatically links articles and notes based on its content. Is this correct? I know that Evernote Premium adds context to your notes so that when you open a note it automatically shows notes that might be related. For more visual links between information I use mind-maps. For this I use ...
You can try out eXtrigo.com they've strong search engine because they need it to provide crowd wisdom for their users. the only problem is to filter out notes from other users and for that you can use your own unique tag for example: #Davidsnotes22 then just search: "Search query" + #Davidsnotes22
I have been experimenting with DEVONthink for a while and it seems it offers some kind of smart links between notes and documents based on their contents. As they write on their website: "DEVONthink is smart. It not only searches all your documents almost instantaneously, it also finds connections between them, extracts the most relevant topic words, or ...
Top 50 recent answers are included