Thanks for the great suggestions everyone! I will use some (or all) of them in my next games. Keep the good ideas coming!
My favorite challenge so far is the 3x5 farm plot challenge, which means seeing how large/long you can grow your fort using 15 squares of farm plot as your only source of food and income. (I've also tried a 7-square challenge and in my opinion that was enough for food or industry, but not both.) Fertilizer is allowed (15 squares is optimum size for 4 bars of potash per season) and trading roasts is allowed. Animals, fishing, and herbalism are not allowed.
I also really enjoyed the 1,000 rock nut challenge which is to embark with some stone (for querns, mechanisms, and jugs) and 1,000 rock nuts. Dwarfs are allowed to gather wild plants and keep animals & bees for their own subsistence, but plot farming is forbidden. A team of millers and pressers spends the spring and summer months processing the rock nuts to oil and press cakes, which are then cooked into biscuits consisting of exactly 1 press cake and 1 unit oil. These biscuits are the fortress's only trade good, and naturally rock nuts must be obtained through trade each year to keep the cycle going.
My least favorite agricultural challenge was anything having to do with bees. The reason is that honey does not stack like plants, therefore you need 5 barrels of mead [5] (not to mention 5 brewing jobs, 5 hauling jobs, 5 pressing jobs, etc) to equal 1 barrel of dwarven wine [25]. It's just annoying and inefficient. Furthermore royal jellies are bugged so you need to micro-manage your stockpiles to cook with them. It's just not worth it (except as a "fun" challenge) in a world where plump helmets are so bountiful!