For about the last decade I've done;
Small => Green
Medium => Red
Large => Purple
PPC => Blue
I prefer consistency of color so you always know what the weapon is (although as previously stated, BattleTech is not WYSIWYG), and I only jewel the laser if it is about to fire (Think "Moment it time", where the pilot isn't Alpha striking but selecting weapons to hit a specific target)... Two good examples are my TDR-5SS Thunderbolts. One is using it's PPC, the other Flamer/x3 Medium Laser/SRM-6. Even if I hadn't reposed them, the difference in what I painted would have helped to make each unique.
Caz