My group is planning on running an Underdark story arc soon. I've come up with some ideas for side/main quest for the Underdark, but I'm wondering if anyone has any good ones to suggest to me to add to the list?
The Underdark is usually not easy to access from the surface, and vice versa. Somebody is trying to create lots of openings. This will be a strategic nightmare because now everybody has to consider being outflanked or threatened from below.
Your job is to make a public and messy end of whoever is doing this, as a lesson to others.
Or your job is to help perform a ritual so most stone between the shallow surface and the deep underdark is too hard to dig through, and resistant to magical efforts to penetrate it. (Sandstone to granite, say)
Or your job is to go down and manipulate several factions into fighting each other (for control?) instead of cooperating on the Opening project.
No I don't like the Underdark and wish it would just go away. 
One thing I liked about the underdark was how they flipped character tropes. Elves (drow) and dwarves (duergar) are evil, for example. So mix it up yourself. Have the party meet some underground sprites (anyone remember the jermlaine?) who want the party to help eradicate a den of albino trolls. However, these albino trolls are actually decent folk, but weak and starving becasue the smaller creatures are stealing their food and the larger monsters can't chase them through the smaller tunnels. The party has to figure out how to tackle the smaller foes in smaller tunnels. Put in some magic mushrooms that will make players smaller so they can battle the tiny enemies, with a time limit. Add some spice by having the underground sprites steal a very important quest item from the party, and don't forget that ants and other small monsters could suddenly become horribly dangerous!
I also loved using myconids ever since the old Slavers series. The ability to create Spore Servants can open up a world of possibilities to use all sorts of monsters in different ways. Maybe there's a magic water source in myconid territory that's needed, and the party has to hack through everything from umber hulks to troglodytes and maybe even a "spored" beholder guarding the magic pool!
Two ideas off the top of my head. Good luck!
Using the drow in general is a nice idea, and you could get a lot of help researching their cities and lore around them.
Beholders and Mindflayers are in themselves a worthy menace that could have an evil goal that be hard for a mere mortal to understand at first.
The following links might help you out:
Depending on where you place your PC's, here is a map of the Underdark
Here is another thread about encounters in the Underdark
A guy giving tips on Underdark campaigns
Furthermore, if you won't be starting this Underdark campaign real soon, I'd suggest you wait or at least try to incorporate the new Rage of Demons campaign into your own, that WotC is releasing this autumn: Rage of Demons
THanks for all your ideas and tips guys!
The playtest adventure Blingdenstone had a side trek that I expanded and it worked well. Basically it was a journey to an underdark trading village. The pcs had to try to purchase a rare root for the deep gnomes because the trading hub was run by drow, dark dwarves and a mind flayer who was the most powerful faction. Deep gnomes were considered enemies to all those factions so it was up to the pcs.
This gave the party a chance to explore, interact and combat. They ultimately conducted telepathic negotiations withe the cloaked mind flayer. This scene freaked them out. They were able to get the root, but the mind flayer sold them out to the drow (telling the local drow that this party had indeed killed other drow). As they were leaving to journey back to the deep gnome village, they were hunted by the drow and their allies. It was a tense and bloody trip back, but the party made it.