Troglodytes are the stinky lizardfolk. (That’s the short version, at least.) They were noted in 1e and 2e AD&D for having a particularly lazy deity, which was good and bad for his shamans (good: he didn’t demand the harsh rites many other humanoid deities did; bad: if he did notice you, he or one of his minions would probably eat you). They made it to the PC level in the (amazing) 3.5 Forgotten Realms sourcebook Serpent Kingdoms. In Pathfinder, they are subterranean degenerates with a strong religious bent. The lucky ones still live in the shadows of their ancient empires; the unlucky ones are slaves of drow and worse.
So for the most part, troglodytes are going to be spear-carriers (well, javelin-carriers) and cannon fodder in your campaigns. But they still have things going for them, namely:
That stench: Trogs are low-CR monsters for low-CR parties. At 1st level, the sickened condition (“–2 penalty on all attack rolls, weapon damage rolls, saving throws, skill checks, and ability checks”) really matters. Play up the choking, gagging, retching experience of fighting these reptilians...especially when it makes a PC just miss his or her roll.
Rocky terrain: Trogs are stealthier in rocky areas, so encounters should feature lots of ambushes. Granted, their stench diminishes the surprise factor up close, but with 90 ft. darkvision they’re happy to stay at javelin range. (Plus, trogs aren’t intellectuals but they’re not stupid either….I can easily imagine them hiding under ratty gray blankets to conceal their forms and their odor, then bursting out of hiding to attack, reeking of death.
Planning and tactics: Once PCs have encountered the above, they should be encouraged to come up with ways to counter those advantages. If the party starts working overtime to attack trogs only at missile range or stock up on alchemical cures or use the trogs’ stench to track them (or mask their own presences) they should be rewarded.
Religion: Heavily religious natures plus isolation/fall to savagery means heterodoxy and fractiousness. Every troglodyte tribe might have a different deity, demon lord, animist totem, etc. Which means lots of excuses for you to customize spell lists, cult powers, religious iconography, and so forth. (Not to mention really creepy/savage animal companions for the druids.)
Lost empires: Discovering that an ancient city used to be a troglodyte city is a great low-level mystery, which could lead—“But if that’s true…what happened to them?”—to great mid-level mysteries.
Reversed expectations: Have you stuck to a pattern of dumb trogs? Then throw some smart trogs at the PCs. That ought to first terrify and then intrigue them.
Or you can do none of the above. Sometimes, you just need someone to carry a spear. Or at least farm House D’Cherith’s mushroom plantation.
A well in the caverns below Choirstone is known to lead to a faerie grotto with magical properties. But fresh water in the Land Below is rare, and bone-armored troglodytes have claimed the well.
A city-state of nagaji features altar-topped ziggurats, lizard-headed statues, and canals that dive deep into the earth. But the nagaji didn’t found this city, as they suppose—their troglodyte slaves did. A charismatic troglodyte shaman begins to rouse his kinsman to take back what is rightfully theirs. The nagaji, caught unprepared, ask outside adventurers for help clearing the shaman out of the stinking sewers where he resides.
Surrounded as they are by dangerous neighbors, subterranean magicks, and the reminders of their own fallen grandeur, troglodytes cling to whatever numinous scraps of the divine they can access. Magred is an exiled dwarven deity who answers the prayers of subterranean outcasts, the cursed, and cave lizard riders; his patronage of less violent troglodyte tribes has kept his divine spark flickering. The Severed Tail tribe worships the demon patron of their drow masters, sewing on the remnants of their shed skin to their shoulders in honor of his flaying knives. Cultists of the Great Old One Bokrug spend much of their time in mushroom-induced hallucinogenic hazes, dreaming of storms over a lake of some other reality entirely.
—Pathfinder Bestiary 267