For folders + their navigation, you can use my addon QuickFolders; it added several productivity enhancements, such as Tabs for folders, mouseless navigation (jump to or move mail to by entering folder name), bookmarks to emails (reading list) that make it very easy to navigate the folder tree.
In my own experience, traversing the folder tree was wasting too much of my time, with QuickFolders you can completely omit that. I have about 400 folders and I do almost never use the tree; especially not for categorizing / filing emails or navigating through my folders; this can be done exclusively with QuickFolders.
Having to use Outlook at work I really experience finding and navigating Emails is a lot slower and more cumbersome there than on my Thunderbird.
Another addon I have written is an assistant for generating new mail filters (outlook calls them rules) - with quickFilters this greatly simplified.
Finally there are some good addons out there for making it easier to do standard replies to emails; check out Stationery and SmartTemplate4 for this.
I think Thunderbird's weak point is in fact the composer, which is a pity because it can display 100% standards compatible CSS3. Due to using Mozilla's superior Gecko engine Thunderbird is very well suited for handling html emails, but the feature set of Thunderbird Composer (which comes from the mozilla central build so it basically a firefox feature) is sadly lacking a lot of features.
I am hoping that there will be some ground breaking improvements in the next 2 years, if not I will start writing some addons for addressing this gap.