Making VIAs: Well, this isn't the best solution on Earth...in fact, there are specialized tools and vias made just for this sort of thing. Of course, I don't have the money for that (not to mention I don't know where the heck to find them) so, when I saw some teeny, tiny nails at the hobby store (in the section with the doll house furniture) I grabbed some to test.

They seem to work quite well. The nails are just 4mm long and the heads are ummm, well I'm not entirely sure. They heads ALMOST fit thru the holes on the perfboard. Anyway, on the left you see the drill bit I used, the nail and the drilled hole (the nail is pointing to it). On the right you can sort of see it soldered in. Unfortunately my camera won't let me take pictures close enough to get the detail necessary to tell the difference between the nail just sitting in the hole and with all the solder around it. Anyway, there it is. The important thing about the nail head is that unlike tiny sections of wire...when you're soldering on the OTHER side of the PCB, the solder won't pull the little nail out (like it will a tiny piece of wire). All you have to do is pick a side, solder in your vias...then flip it over (the flat surface the PCB is sitting on will prevent them pushing out) and solder the other side. Presto, a fairly nice (and very small) via. You can even use a desoldering braid to remove excess solder (it won't remove it from underneath the head) to make the vias look really neat and tidy (well, on one side anyway)

Heat shrinking bottles: I'm also going to give heat shrinking a 2liter bottle a shot. I'd LIKE to get it shrunk down to the point that it fits a piece of 2inch PVC. Not sure if that's going to work but you'll never find out without trying :) Anyway, here's a crappy looking pic of it