Ink layer order

There is no surefire order for layering riso inks when overprinting—unlike something like screenprinting or offset which have hard and fast rules (usually light to dark). However, there are multiple rules of thumb which can provide some guidance.

General logic

The standard modes of color order are:

Least coverage to highest coverage — This is most important in the center strip (which is prone to roller marks) and the lead edge of the page (which is under the highest pressure when feeding). By laying down low coverage layers first, the feed tires will pick up less ink for subsequent passes. If there is no ink at all in the center strip (perhaps it is the blank inside margin of a 2-up or 4-up layout) the next color can be put down immediately (assuming there are no wet-on-wet considerations—see below).
Opaque colors before transparent colors — Some riso inks are more opaque than others (particularly those that use a "white base"), such as Cornflower Sunflower Mint Bisque Metallic Gold etc. These are often printed first, so that they don't block out the colors beneath them (unless that is the desired effect).
Pinks and reds last — The warm pigments, especially Fluorescent Pink and Bright Red tend to be the slowest to dry. So doing these towards the end of the order will decrease the likelihood of messy roller marks.
'Yellow last — Due to something in its chemical composition, Yellow tends to act as a resist to other ink colors printed on top of it. The colors get slightly muddier, losing their vibrancy. This property doesn't seem to be observed in any other inks.
Desired ink for "color grading" at the very last — In overprinted colors, whichever color is put down last will often shift the hue slightly in that direction, creating a form of "color grading" (i.e. in a CMY separation, if the yellow is printed last the image will be slightly warmer, if the cyan is printed last it will be cooler). This can be tested by changing the order of a multicolor print, and observing the difference in the final outcome.