Almost all of my internal cuts are done with a jigsaw, which usually explains why they end up looking rougher than normal cuts. If I wanted to cut a box for instance, I'd draw the box, add a chamfer on all the edges with a 4mm radius, then use a centerpiece tool to find the center of the chamfer. From there, I print out the part and drill 8mm holes at each chamfer location. These holes allow me to fit in the jigsaw blade, while also reducing the likelihood of the corners being points of failure. From there I just cut, usually back and forth as I'll be a little off where the line starts due to the size of the hole. Trickiest part here is clamping the piece down, as the clamps cannot interfere with the jigsaw, itself taking an awful lot of space up.

Forstner bits look like a good option for future holes, I'll definitely keep my eye on them for future builds.