My ordering is roughly similar to Bickendan's. It's based largely on when route systems were added to CHM (which started with Interstates, then expanded into US routes and other systems) and TM.
-- Interstates (regular then business then future), by state with the states ordered more or less from west to east
-- provincial freeway systems (ON, QC, NS)
-- U.S. routes, ordered similar to Interstates with some variances in the state order depending on how hard it was to reconstruct my travels in those states
-- TCH
-- "select" freeway sets in the U.S., except numbered freeways sometimes got moved to state route sets when they went active or into preview
-- state/provincial routes, in order of when those route sets were rolled out in at least preview
-- national park and some historic highways, by state in more or less random order
-- Mexican and European routes go at the end, no matter when they were rolled out
There's enough inconsistency in my entry order that I often need to do a Wordpad search within my list file to find where in the file I put them, or where to add new entries.
One other thing I do is try to group together entries for a route within a state, in order of where they show up in the Highway Browser. That makes it easier for me to fold entries together when I fill the gaps between them. Some trips focused on such gap-filling shortened my list file while covering more mileage.
Also, I try to remove or avoid adding list file entries that are entirely concurrent with other routes (in early CHM days, we needed such duplicate entries, but now automatic multiplex detection makes them unnecessary). For example, many Texas Interstates are concurrent with U.S. routes, so I just list the U.S. routes without duplicate entries for the Interstates.
