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In general, the minimum vertical distance two IFR aircraft can be (if they are not separated laterally) is 1,000 feet. This allows for inaccuracies, for example due to:
altimeter error
instrumentation imprecision
pilot imprecision
turbulence
aircraft height (compare a Skyhawk, nine feet tall, with an A380, 79 feet tall)
while still making sure aircraft do ...
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This answer is specifically for the US--
Above 3000' AGL and below 18000' MSL (which is not the same thing as FL 180)1, cruising VFR traffic flies at MSL altitudes which are "round" numbers plus 500' (e.g. 3500' MSL, 4500' MSL, 5500' MSL, etc) while cruising IFR traffic flies at MSL altitudes which are "round" numbers (e.g. 4000' MSL, ...
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