hrm.. this is an interesting topic actually.
I know one thing I have thought that would be interesting is to have the mobs scale to not only the difficulty but the highest level of the party members.
For instance if you take a group of level 14's into waterworks.. the kobolds and trogs are CR 20+.
another thought I was thinking about is having an option over elite that had some random effect for the quest. I have been playing around with Eberron Cosmology lately and all the differnent planes of Eberron. Why not have an option above elite that engages a manifest zone. For example, you set waterworks quest to Coterminus (or whatever you want to call it) and you get the waterworks quest inside a manifest zone for one of the planes.. for example.. trying to free Arlos in the middle of a Shavarath manifest zone.
Here is an example of one of the planes from wotc:
Shavarath, the Battleground
Three great armies mass eternally on the barren plains of Shavarath: a celestial host of archons, an infernal regiment of devils, and a swarming horde of demons. Warfare defines all aspects of their existence. Alliances come and go -- usually involving the devils allying with one or the other of their enemies and then breaking the alliance when the situation changes to their advantage -- but the warfare never ends. Slain soldiers eventually return, usually in a lower form, but the armies of the three forces remain forever in a rough balance.
Enhanced magic: Spells that create, enhance, or mimic weapons (such as flame blade, keen edge, or Mordenkainen's sword), and spells that excite hostile emotions (such as rage, heroism, or antipathy) are extended.
Impeded magic: Compulsions that calm or pacify hostile creatures, and all charms, are impeded.
Whirling Blades: Creatures not native to Shavarath are subject to attack by whirling blades that travel the plane like flocks of birds. An attack occurs every round once a flock of whirling blades is encountered (70% chance): attack bonus +10 melee (2d6). The blades are treated as magic and evil-aligned weapons for the purpose of bypassing damage reduction.
Coterminous: When Shavarath draws near, echoes of its endless battles manifest on the Material Plane. In any area embroiled in combat, the enhanced and impeded magic traits of Shavarath spill onto the Material Plane (impeded spells require a Spellcraft check, DC 15 + spell level to cast). Also, storms of whirling blades are known to appear at the sites of great battles, both past and present, when Shavarath is coterminous.
anyhow just an idea i had about a crazy level above elite that would weave in some Eberron Lore as well as provide some crazy battles.