What kinds of gaps/tolerances should I use when designing pieces that fit together? Let's say I'm modeling a simple box with a lid. Just as an example, we'll say the outer edge along the top of the box is 50mm x 50mm. With 3D modeling software, it's easy to build a lid for this box to surround the top with an inner edge size of also exactly 50mm x 50mm ...but this seems like a bad idea. Surely I'll want some kind of of gap, to ensure an easy on/off. An exact fit seems like it's asking for trouble.


How much gap do we leave for this kind of thing? 
Is it related to nozzle size? 
I suppose it also matters how tightly you want to fit, though I expect in cases where a tight fit matters some kind of snap or clip would be used. 
Are draft prints with larger layer sizes useful for figuring this, or do the rough layers make things seem tighter than they'll be in a final print?
I use my clearance values according to my rule of thumb: 0.1mm - to fit with some force, 0.2mm - just fit edge to edge without force.

Examples:

1) 3mm metal cylinder to be pressed into plastic part needs 3mm+0.1mm*2=3.2mm diameter printed hole (clearance from two sides)

2) 3mm screw to fit into plastic part needs hole bigger than 3mm+0.2mm*2=3.4mm that is 3.5mm will be already good.

This is fully experimental but always worked for me on three different printers and both on PLA and ABS.