I've come to notice some nice design patterns while building parts to work with Metric hardware, and I thought I would share.  

Simple stuff, but it ends up meaning I need to keep less stuff in my brain while doing it.  That is usually a good thing.

Size as used here is just the M number of the part, such as M3, M4.  Size is expressed as a diameter, with most OpenSCAD operations using radius, so <dia>/2.

Clearance as used here is always 0.2mm, and that number came to be to allow over-extruding while printing to not affect the fit of the final parts.

1. Through holes bolt sizes are just <size> + <clearance>.  So a cylinder to subtract for a bolt hole is:

   cylinder(r=(size+clearance)/2,center=true);

2. Pan heads are always 2*<size> + <clearance> for diameter, and <size> for height.  So a cylinder to subtract to flush fit the head of a bolt would be: 

   cylinder(r=size+clearance/2,h=size,center=true);

3. Encapsulating a nut or bolt head is just as easy.  Nuts are the same dimensions as pan heads, but you limit the cylinder to 6 facets.  The cylinder with 6 facets still has its vertices on the ideal cylinder, but the flats end up moving in the same as a nut.  So a cylinder to subtract to create a captive nut is just:

   cylinder(r=size+clearance/2,h=size,$fn=6,center=true);

4. Threaded holes are <size> *0.9.  So a cylinder to accept directly threading in a bolt is just:

   cylinder(r=size*0.9/2,center=true);

That's it.  Four simple rules and can you can use any metric hardware without measuring.  I've never actually looked up if there is a specification which matches these observations, but so far so good.