I never did come across any handy dandy advice for laying these out, so I thought I'd share what worked, leaving out all my tales of woe about what I did wrong before I discovered this method.
If I had it all to do over again, I would have started with a much more simple beginning than I did, so I suggest you do as I say, rather than I did. Mark one line perpendicular to the front of your bench. Now measure the first and second courses of dog holes and mark two lines parallel to the front of your bench.
Mark these two holes very carefully with an awl. You could do three or more holes as well. More holes further apart will probably make for more accuracy later.
Now find a piece of perf board with 1/8" holes. Bigger is better. The one I had on-hand was large enough to mark six hole locations, but I think it would have been more accurate if it had been both longer and wider.
Pick a corner hole and circle it. Measure the distance between centers in the perf board. 1" is probably standard. That's what mine was. Now mark out as many holes as you can, spaced out at your target distance. For six inch centers with 1" hole spacing, you need five empty holes between every circled one. (If you're going for 7 3/4" spacing or something like that, then you'll have to figure out something else--this method is useless to you.)
Now find some nails that are as close to 1/8" in diameter as you can manage. Poke a nail through your first circled corner, then tap it into the first hole you marked with your awl. You want the nail to stick, but you don't want it to be difficult to remove.
Spin the perf board around until you're lined up with the other hole(s) you marked on your line and then tap another nail into this one. Now tap nails into the centers of the remaining circled holes, using as much care as humanly possible to ensure that the nails go straight into the center.
If you used a big piece of perf board, you might be done already. If you used a smaller one like I did, you'll need to pull up the nails and move it. I suggest moving it so that you re-engage at least four holes, on at least two different courses, which have already been tapped. On my six-hole board that meant I only got two new holes for each move of the perf board, but I feel it increased my chances of accuracy.
When you get to the far edges, have a care to stay within your 3" or whatever margins. Otherwise just tap away. When you're done, you should have a board full of perfectly spaced little dimples that are just the right size to center the spur on a Forstner bit.
I drilled using a hardwood guide I made by boring a piece of scrap on my drill press. It produced satisfactory, though less than perfect results. Some kind of drill guide thingie would probably be preferable.
Anyway, that's what worked. The spacing is still not 100% spot on, but it's close enough that the slop factor from slightly wallowed out hand-drilled holes gives me enough lateral play to make things fit between any two holes without having to take a hammer to anything.
If for some reason you're one of the people out there who hasn't gotten around to drilling dog holes yet (why else would you have read this far? :) then you'll really be glad you did once you've done it. Dog holes are awesome!
Well, I hope this helps someone. Everyone feel free to chime in with suggestions for improvement or to just generally point out that I did this a stupid way, and I should never have posted this message.