On my 93 22re which is a california model, one hole is plugged, the second goes to the vsv that controls the fuel pressure regulator, and the third one goes to the vsv that works with the EGR.
My bet is that hole should just have a plug on it unless cruise control has something to do with it. Have you looked at the vacume system routing info on the underside of your hood. That should tell you if anything should go there.

"4X4 in upper case is $X$" Quoted from http://4crawler.com/4Runner.shtml
'00 tacoma 4WD---Sold to Toyota
'93 pickup 2WD
'85 pickup 4WD