A couple of times...
In an old FR campaign, the PCs recovered an ancient dwarven book of "blueprints" laying out the design for a number of advanced weapons. One was a wheeled ballista platform with scythed-wheels and crank-driven reloading device (a 4-dwarf team). After a lot of trial and error, they created a working model with the help of the local dwarf clan and become famous for clearing goblin infested tunnels.
My kobolds tend to like setting up ballistas at the end of long, straight narrow tunnels...
In my most recent Faded Glory campaign, I designed a rather nasty undead ballista. The ballista fired mummified zombie heads that were attached to the ballista by "lines" made from woven intestine. On a successful hit, the zombie head would attempt to bore into the victim, at which point the skeletal ballista team would start reeling the victim towards his/her doom. It was particularly effective at preventing casters from getting of spells without a serious concentration check from continuous damage...yummy!
~ OO
PS - Have usually used the ranged touch attack rules with siege engines, but made them a single exotic weapon proficiency for each siege engine (with double the non-proficiency penalties).