I would think a decent single-board PC with flash drive running some stripped-down version of Linux would be an excellent, and relatively inexpensive, controller system for the entire setup. A unit with sleep mode would also draw minimal power when not running. You could still use the controllers for I/O and ports, developing a control program in your favorite scripting language (PHP, perl, etc.) wouldn't be too difficult, and you'd have all the logical capability you require, including interrupts.
Take a look at Circuit Cellar magazine/web site. They have many advertisers of such hardware.
http://www.circuitcellar.com/
http://www.circuitcellar.com/suppliers%5Fdir/SBC.asp