The idea is that you could organise your selection of bookmarks, like you can in a selected folder and sub-folder of your operating system. EX List (music) in différents folders (classic, rock, ...)

Annotation on PDF document

The only feature that delicious has and that I regret Diigo hasn't

Add ability to color-code tags, similar to gmail's labels.

This might not be useful for all, and it's probably a "maybe later" feature. But Gmail style filters would be really useful.

Eg:

If tagged A and B but not C, add to list L1 and submit to group G3
If tagged F and unread, add to list L3.
If tagged G and H and read, add to list L4, add tags T1 and T2, submit to Twitter and Submit to blog.

Diigo is a great tool for collecting information, in order to be more useful in the academia, it should offer creation of bibliography and citations according to accepted formatting rules used in journals and publications. Tools that already have these features and somewhat overlap with Diigo are for instance Mendeley, Endnote Web or NoodleBib.

I have multiple related tags that I would like to relate under a common tag.
something similar to gmail folders:
X / bla
X / bla2
Y / bla3
this way would be easier to categorize items.

All tagged items could be linked together through semantic relationships such as: "evidence for", "argument against", "relies on", etc. This could potentially culminate in a concept map mode—displaying the web of connections around particular tagged items.

1000 Characters, minimum. Right now, all my delicious imports are being chopped off, which is going to mean a LOT of work on my end.

Another way to re-contextualize your data. Essentially, notes would have wiki-level functionality (whether private or collaborative) and drag-and-drop or auto-complete-as-you-type access to your entire database of tagged items (in the form of links).

Would really appreciate the ability to do mass editing of tags, it's easy enough to add new tags, and replace all tags with new ones but no easy way to remove tags.

May I suggest you add a new feature under 'Revise Tags' to do a search and replace / remove, but instead of searching you list all tags and allow the user to CTRL + Click the relevant tags, then either remove or replace (with either a single tag or multiple)

Great service btw :)

I've seen enough sites get archived and articles moved. Rather than have to delete a bookmark & then re-create it allfrom scratch again, can we be allowed to edit the URL? (Delicious allows this and it's been very useful in the past)

I need to have a way to ensure that things are private unless I share them explicitly. It's 2010 and poor privacy is a deal breaker.

One of the Delicious features I love is the ability to flag a bookmark to one or more friends. It would be great if diigo had similar functionality without needing to set up one or more groups.