Remnote is a powerful notes taking program which is available both as on online version and as a web application.
Key features of the applications are - Ability to link notes - Configuring notes for space repetition - Good PDF notes taking editor which allows to take notes while reading a document. - Defining your own templates to structure your notes - Pleasant UI for all you notes.
Complete details of all the features are available on the RemNotes Website
There are other options, however, in my view Remnote is the best. I believe I was one of the early adopters and I have seen the evolution over the years. Continuously new features are being added and this has greatly improved the overall value proposition offered by Remnote.
Lastly you can try the application using this link. This will give me some credit, however, seeking credit is not the reason to post this link. I genuinely love Remnote and I believe it one the best tool.