In most pokedexes, legendary pokemon are listed last.
Example
In gen 1, mewtwo and mew are last.
However, there're some non legendary pokemon that appear amongst the legendarys.
In gen 1 dratini and it's evolutions appears between moltres and mewtwo. In gen 2, larvitar and it's evolutions appear between Suicune and lugia. Why?
I believe it's because the developers had no idea what they were doing and were pretty much just winging it for the first few gens.
The spots where the Dratini and Larvitar lines are probably placed there to signify that they are pseudo Legendaries and that they evolve at higher levels than most Pokemon. Gen 4 is the exception of course.