I normally divide buses by town served (or major town, if they visit more than one), trucks by cargo, ships by cargo and/or type (so, "Bulk Cargos" for Iron Ore, Coal, Grain etc, "Piece Cargos" for Steel, Timber etc), and planes by route and length (so, "Hoppers", "Short Ranged" "Medium Range" "Long Range" "Ultra-Long Range" then by route in those categories).
Trains and trams get complex. They depend on time period, initially being divided first into railway operating company (LNWR, Midland, LSWR, GNR etc) then by either Goods, Passenger & Mail or "Reserve" (where I keep spare engines that are not life or use expired), then for Goods its separated by type (a bit like ships, but usually Mineral & Aggregate Traffic, Heavy Goods like steel, timber, Manufactured Goods for Goods, Manfacturing Supplies etc, Farms & Produce for anything grown etc) and for Passenger & Mail separated by route then type, so Passenger first then Mail on that route as a subgroup.
Of course, with the coming of Nationalisation, the operating companies become Regions (and bits get chopped and changed around before then anyway), and in the 80s, Sectorisation comes in so everything is divided by what BR sector they are part of. (Different Railfreight sectors, Regional Railways, Network Southeast, Scotrail...)