Do you have or did you come across any documented methods/procedures/best practices for Diigo? I've researched high and low and I did find some but not quite at the level I expect. If you've come across any good ones, kindly share. Thanks

I would! I actually have the same frustration.

At the moment, I simply add ...
1. a list tag (ie. "bk" for a list pertaining to my book)
2. a structured tag (ie. "bk-training-entrepreneurship") so I can easily find all the trainings related to entrepreneurship that I bookmarked specifically for my book project

The above works for me. But it is quite cumbersome to have to remember to always add above additional tags. If anyone has a better method, kindly share.

Also, at the left of the list, we should have visibility for the most common tags for that particular list.

I use lists practically for all my projects. I create lists way ahead I actually start a project so I can dump in there as much information/ research materials as possible. The problem is by the time I am about to actually start on the project I have way over a hundred bookmarks. While I try to maintain consistent tagging and a structured tag (ie. mentioned above), it is still difficult for me to remember all the key tags/category/division I used for the project. The work around ofcourse is to maintain a separate list/manually enter the key tags in the list description. But this is very crude and cumbersome. Now if I can easily see the top tags used within the list, that would make my processing much much faster!