Foxface's collaborative campaign world
Bawylie's assortment of DMing and storytelling tips threads
That one where Hobo Delight answered everyone's questions with professional regularity
Any others?
I wasn't here back then, so I missed all of them, but since I haven't seen them I can't say that I miss them 
(Useless post about semantics is useless)
The threads themselves still technically exist (and you can still post in them too). They're just hard to find.
Here's Ramzour's "Class Defining Abilities System" thread, by way of example.
The random trinket table.
pauln6 wrote:
Homebrew Psion -TaalVastal
I miss every thread that wasn't a debate over WotC's business practices, sales of various editions, the HP/Alignment/DS tar-babies, or nitpicking rules apart.
I miss Orzel's and Lawolf's home brew classes. Emerikol's long winded and evolving refinement of his play style. Ren's left-field hypotheticals. Honest pleas for advice. How would you rule?s. And campaign/adventure sharing. Neat tools or ways of thinking I hadn't come across.
And I miss a few fine folk who won't be back, for various reasons.
Flavourful Magic Items - I enjoyed that.
The collaborative campaign thread has been saved in document form. It will come back in some form in the future. Life is busy.
I miss Lokiare. While I didn't always agree with him, I valued his questioning of commonly held, unsubstatiated beliefs regarding D&D. Such a person is worth 1,000 people who like a product, for the latter won't help you make positive changes to appeal to a broader audience due a yesman echo chamber effect.