In nearly every hard or deadly encounter I designate 1 of the bad guys to be the squad leader/captain. I'll buff his hit points and give him a feat or special ability. I really like using even just 2 or 3 levels in a class also.
Having the monsters work differently than PCs is awesome. For monsters, there is no wrong way to make a foe. It is liberating and encourages creativity.
I think the key is to understand some of the bigger ways that creature abilities affect CR. Giving a monster spellcasting ability (especially area attacks or crowd control spells), breathe weapons/area attacks, petrification, death gazes, etc., make an encounter more difficult. Other than that, a lightly modified monster in a group -- one with 25% more hit points, maybe slightly better armor and a feat-like ability, only changes the encounter a little bit...mostly to make it more surprising for the players, not so much more difficult.
Since I run nearly all my games online using Fantasy Grounds, I even let the tabletop generate random hit points for most of the foes so that the players never truly know how easy or hard it will be to hurt even the lone bugbear.