if the holes are electrically connected I would place a component in the schematic (as Stuart suggests) otherwise I just place them in the PCB.
For mounting hardware I have created a series of footprint for standoffs and nuts with washers. I usually load these with file -> load element-data to paste buffer (or I use a script to place them at specified locations). The footprints are at --- http://www.luciani.org/geda/pcb/pcb-footprint-list.html#Hardware (* jcl *) -- http://www.luciani.org
