I think this is a moving target, perhaps it always will be, because of the number of collaboration tools that seem to multiply daily.
Anything "cloud-like" can be an issue with IP and concerns about control and storing company information remotely. And some times there are contracts where you have to be able to prove access or inability to access (military, government etc.)
It has to work for the people involved, just like you are finding paper to be a break in the work flow, any new tool , even on the keyboard can be as intrusive to someone else. I've found that the tool that gets used, no matter how kludgy was the best one. Just make sure that the "database" is human readable and portable, so some sort of markup or markdown aspect, so that when you change and adapt things can be ported over.
What has worked well in the past is a combination of Wiki, bugtracker and SVN band-aided together. The bugtracker tied into the Wiki nicely and soon because a Incident, Idea and To-Do list. The Wiki took in extra documentation, *.pdf's, Notes, meeting minutes, pictures from white boards and SVN (I suppose now you'd use Git) was used not just for source code but even internal documents and revision control with log stamps (which are necessary for legal reasons).
Something that is browser based and able to re-sync upon attachment is advisable so you can work off line.
Most importantly it can't be a bureaucratic response i.e. "thou must write this way" rather it's better to say "You know that Jill likes to dump meeting minutes into the revision control, you like the wiki - make sure there are obvious links for her to find what you write and vice versa" what would evolve is that a top level calendar appeared with meetings and links to notes. And here a meeting might be two people brainstorming at a white board with pictures to an official launch meeting. If it was easy to use, people would gravitate to it. With different teams having different compositions it's hard to predict how to best compose the tools, so be flexible.
I've looked at Asana and various on line tools for remote collaboration and they seem to be too inflexible and the cloud aspect is an issue for security. Evernote is handy, so snipping clean shots and down loading to a local *.pdf to be dumped into a wiki seems to work best for the occasional web reference, I couldn't use Evernote for any other than just web snaps.
Huge design databases get siloed separately, but with repository information being dumped into wiki's via scripts for ease of search.