+1 here.
After starting to use OpenGoo deeper and moving all the organization's tracking over there, comments are often used to follow up a ticket publicly and take a decision on it. The lack of a comment referencing has almost immediately popped up as a demand.
"Nesting" would be great, but I think a "reference to" possibility might already solve 80% of the problems with 5% of the effort:
1) you have already provided a (reference-able indexing for comments: #1, #2, ...)
2) you parse comments' content: when -- say -- @#2 is found, you can
a) render it with a tooltip containing the raw-text of the referenced comment, eg with a plain "title" attribute
b) render it as an hyperlink to the referenced comment
This should come quite cheap to implement and already solve most of it, ie it works for 10-15 comments. If you sort comments by referencing rather than by date (ie #5 comes after #2 because it references #2), without necessarily "nesting" or other layout mods, this could work also for 50 or more. I can contribute code for computing the order that you can include for this, if you are interested (using plain topological sort).
If comments are used seriously on the platform, I think this feature is really hot, almost essential.
What do you think of this?