How much do spokes stretch when first used? I built a wheel for the first time recently, so I checked it after a few hundred km. The spokes seemed to all have lower tension (by pitch) than when I built the wheel. I tightened them all about 1/4 turn (except one  that needed more) and had to slightly retrue one section of the wheel.

I assume this even loosening was due to the spokes stretching, but do they stretch significantly after the wheel is trued? Should I build it to a slightly higher tension/pitch than I expect to run long term?
They don't. Spoke stretch is a very theoretical effect that mainly happens when tensioning loose spokes or over seriously long term usage.

What you have experienced here is most likely due to the spokes finding their final place and form, possibly combined with twisted spokes working their ways straight. These are common and expected things especially when using the J-bend spokes, but they can be migitated, although not by over-torquing the spokes as you suggest.

New J-bend tend to leave the hub at an angle parallel to the hub flange, but obviously they'll end up with a bit of an inwards angle to meet the rim. Before tensioning, when all the spokes are in place, you can gently push each of the outer spokes inwards where they leave the hub, thus deforming the spoke a bit and causing it to have the proper angle even before tension is applied. If you don't, some of the tension may be lost afterwards when the tension itself causes this deformation.

Additionally, spokes may twist when tensioning. This applies to all spokes, but is of course harder to spot with round ones. What you need to do is lubricate the spoke threads beforehand, try and hold the spokes with appropriate pliers when tensioning them, and most importantly, you should try to release this torsional tension during the wheelbuilding process so you can re-check and adjust accordingly. 

Releasing this tension happens by grabbing two spokes where they cross and squeezing them together, or by grabbing the rim at opposite sides and pushing the hub/axle against something. You'll hear slight 'pings' when it happens. Reiterate for both sides of the wheel, on multiple different spots on the rim.