Lacing 40 hole rim to 36 hole hub.
 

How can I do this?

Why would you do this?

Check this out
http://sheldonbrown.com/mismatch/index.htm

With great care and some concern.
The other way around would have been "safer", as the rim would still be evenly supported, and the hub, in this perspective really doesn't care much as long as you avoid radial lacing.

What you're suggesting would leave you with two points on the circumference where you'd have double the distance between spokes when compared to the rest of the rim. It might still work, depending on intended usage, but it will set up a rather interesting load distribution at those points.
Either you can set it up to have the left missing spokes match the right missing spoke, which'd make it reasonably easy to true the wheel and to balance the spoke tension. Or you can stagger the L missing spoke WRT the R missing spoke, which would play merry hell with trueing and spoke tension balancing but would probably result in a stronger wheel.
Thinking a bit more and counting with my fingers I think offsetting the missing spokes would open another set of worms, as it would upset the spoke alignment out of the rim.
Every 2nd hole is aimed at the different flanges, leaving just one empty would cause the spokes to start out aimed for one flange and then bending significantly to reach the other one.
For a fairly flat low-profile rim, preferably with eyelets, this is doable, but if it's a high-profile rim it gets awkward.
The real catch is that you're leaving a bigger portion of the rim unsupported, so I wouldn't even try it for a wheel meant to be used unless the same rim profile is also available in, say 24H drilling.

In practical terms the issue lies in that not all spokes will end up just where they're "meant" to be, so you'll either have to calculate your own spoke lengths, or you'll have to tweak the given values a bit.
If it's a low-flange hub the offset won't be that much, particularly if you stay with 2X or 3X.
If it was me I'd start with drawing up the lace pattern first, which'd tell me whether the spokes closest to the empty holes will need to be longer or shorter than stock. Then I'd calculate the spoke length for a standard 36H and either add or subtract a few mm for the spokes closest to the empty holes.
Closest to the hole might require a 4 mm tweak while 2nd to the hole might do with 2 mm. The rest should lace up fine with standard length for a low-flange hub.

If I really wanted to use a rim with more holes than the hub I think I'd rather cut an adapter plate, basically a wide washer which would fit over the hub flanges. Close to the outside edge I'd drill out a matching number of spoke holes for the rim, and along the inside edge I'd drill holes to match the hub flanges. The adapter plate could then be screwed or riveted to the hub and the wheel cold then be built just like any other matched hub/rim combo.

Hey, that's a good idea. I remember seeing some hubs that were built in three pieces with the outer-flanges being removable for bearing-replacement. Would be simple to get alternative flanges with different drillings.

Well, I've done something similar once when I wanted to stick a Shimano-compatible hub into a composite wheel meant for an IG hub.
For something like this, with the adjustability offered by the spokes, I'm certain one could get sufficient precision by nothing more than hand tools. A drill, a fret saw(scroll saw?), some files and a divider. It would require some time though.