It depends on the cut. Everyone's been focusing on the material.
Sport (for lack of a batter term) pants are close cut and designed to go in the boot.
Jean/Trouser style pants are looser cut and will go on the outside generally.
I've seen some textile sport style pants now and leather 'jeans' - even seen a set of leather bib-overalls... So just let the cut of what you're wearing be the determining factor really.
My Sidi boots work well with my sport leathers inside them and just as well with my armored jeans over them. Lots of folks like Sidi and they make a wider variety of boot, from 3/4 boots for casual street riding, all they way up to GP spec race boots.
Aerostitch has some cool boots as well if you're more into a retro/leather look
http://www.aerostich.com/catalog/US/Combat-Touring-Boots-p-1-c-446.html