Here are a bunch of trolls altered with material from Mutant Future (though several of the mutations are my creations):
Induce mutation, intellectual affinity (pack leader)- these trolls capture goblins and kobolds, infuse them with troll blood and use them as swordfodder. The little ones get 1/3rd strength troll regeneration but die if cut to pieces.
Animate object- stone lords can animate 4 rocks up to 50 per round. They howl and the stones roll to action.
Induce mutation, force grow plants- this is a very nasty troll because of its effects on vegetation. Its blood causes them to deform, grow massive, animate and go on a rampage. Even if the troll is beaten into submission with blunt weapons, it will bleed. Also, take a look at how abundant tree roots are and how far they travel from the trunk.
Diet change, increased strength (environmental dependence), aberrant form (xenomorphism)- these trolls have mouths in their hands and drain blood from their victims. When they feed on elves, they visibly gain muscle mass and do an additional 3d6 points of damage with their claws and bite.
Toxic weapon (narcotic)- some forms of healing potions use troll blood and if it is collected from this troll, they become addicts. Addiction to healing potions may seem funny until you look at the price (more powerful version give a stronger high) and that the potions, slowly, give the consumers troll features.
Reflective epidermis and energy ray- fire trolls absorb heat and breathe fire. Their lairs are always cold with ice on the walls. They are immune to magical fire and heat and gains a small bonus to their own flames for a few rounds after suffering such an attack. The base breath weapon does 4d6 and when augmented, 6d6 for 2d4 rounds.
Alter atomic composition- mud trolls turn metal to mud with a touch. The only difference between them and rust monsters are the trolls' fangs and claws.
Flexable skeleton- now the troll can fit through any hole it can pass its head through. It can also fold its body to hide in small spaces.
Increased balance, new movement type (climb)- a troll that can climb almost any surface and bounce around on buildings like a super.
Spiny growth, temperature control- a porcupine troll can rip off spines, heat or chill them before throwing the quills.
Parasite host, variant of light to mass- this troll grows stronger in sunlight (more HD and damage) but so do the little critters swimming around in it. If slain during the day, the tiny creatures will boil out of hit and attack the party.
Regenerative capacity (environmental dependence)- some trolls only regenerate in certain conditions. Scrags already are restricted to water but they are the tip of the iceberg. Those that require the blood of a specific race or monster, only in light or dark, only after eating or something strange like having a spell of a certain school or sphere cast on it (e.g. evocation spells only make them stronger).
Light to mass- these troll can rip off their own skin and make weapons and tools from it as long as they are exposed to sunlight (or magical radiation). Or they leave globs of bloody goo wherevery they pass. The go isn't dangerous except where it builds up- troll fens can get clogged with the stuff and it kills the plant the trolls rely on for medicine and housing (i.e. they are nomadic).
Metamorph (environmental dependence) or aberrant form (environmental dependence)- these trolls change their form when exposed to something. Day trolls are (very sneaky) goblins by night. Night trolls gains some abilities from dragons (ie half dragon template or something similar) when in moonlight. Sea scrags become massive sea serpents (use purple worm stats) when powerful storms hit the seas. Troll weres are trolls that normally look human. Only when feeding on human blood do they revert to their normal form.
Bizzare appearance (environmental dependence)- these trolls are cursed so that they are driven out of their tribes. Whenever they see holy symbols, they reek of acid and drool heavily, harming themselves (reduce their regeneration to 1 point per round). Or they grow purple fur whenever the temperature falls below freezing (it doesn't help protect them from the cold and easily mats when wet). Or they grow boney spurs when splashed with salt water (AC penalty of 2).
Aberrant form (xenomorphism), thermal vision, increased smell, loss of trait (limbs)- troll worms have no limbs and yet can move just as fast. They hunt by scent and heat and can sneak up on a person unlike a 9' tall troll. Scrag worms are a fisherman's third worst nightmare (after dragon turtles and krakens).
Aberrant form (extra body parts)- sometimes troll regeneration goes wrong. It produces extra limbs, heads, torsos or even organs (trolls with 5 eyes or extra, exterior lungs). Fortunately for the troll, it can simply tear off the extra parts if it wants to.
Flesh pocket, chemical gland (adaptive)- some intelligent trolls use simple alchemy or herbalism. This specific troll can produce minor substances and hold them in its own flesh until needed. No one expects a troll with flash powder or fire slime (it reduces fire damage by 1/4th).
Complete wing development (environmental dependance), increased balance- these trolls are found in mountain ranges. They migrate up from the valleys every spring to just above the tree line and gain functional wings at the start of summer. They do not migrate down willingly. Most end up on the valley floor after crashing as their wings degrade in the late fall. Those that remain in the mountains freeze to death come winter.
Aberrant form (gills, environmental dependance), increased vision (environmental dependance), lack of sleep- these trolls are found on land during the day and active underwater at night. Their eyes actually grow with darkness and shrink with light (though this takes an hour, so provides no benefit against blinding attacks). They travel, and lair, several miles inland and almost never are found near water while the sun is in the sky. The fish that come to the surface to hunt by starlight are favored prey, even over humanoids.
Increased strength (environmental dependance), reflective epidermis (level 1-4 arcane spells, environmental dependance), toxic weapon (activated)- magic consuming trolls, these creatures need to be exposed to large amounts of magic before their abilities kick in. They are significant pests near wizard towers and universities. After being near a spell or effect (they do not have to be targeted), the trolls' damage increased by 3d6 for each claw attack, they become immune to wizard spells below 5th level and their bite gains a 10/50 poison that only affects spellcasters or those being affected by magic (it only lasts 1 minute in the blood).
Aberrant form (xenomorphism), natural armor (variant)- some wizards use trolls to make gems. The trolls have been altered so that they excrete a layer of gemstone on their skin on the limbs and torso. This improves the trolls' armor class by 2, though few are allowed combat. In effect the trolls reduce the cost of the gems by 10-25% as the diet the trolls need to grow gems is quite expensive.
Control weather- as the troll population increases, the climate dries. As some point the desert conditions drive out the trolls and the land reverts, though usually different from what it was before due to erosion and possibly the effects of lots of trolls and people (desert dwelling races follow the trolls in a very slow migration).
Combat empathy, unique sense (5 seconds in the future)- These trolls can outfight even the most experienced monk in hand to hand combat.
Aberrant form (xenomorphism), loss of trait (regeneration, decidious)- like some frogs, fish and invertebrates, these trolls can freeze solid and survive. Come winter, they turn white and look like marble statues. Only those who hide well survive the human population until the spring as shatter trolls can not regenerate.
Aberrant form (natural weapon (decidious), xenomorphism), loss of trait (claw attacks), quickness- known as stag trolls, these creatures like like nightmarish deer. They do not have claw attacks but make this up in the summer and fall with antlers. Both sexes grow these but females (being larger than males) can grow some very lethal "horns". They are just as unrelenting as normal trolls but are much faster and most people and creatures can not outrun them.
Drone- master trolls make smaller creatures from their own flesh. These slave critters look normal on the outside but are shells filled with troll blood.
Metamorph (environmental dependance)- tar trolls are obvious as most have something sticking out of their flesh. Any weapon that hits them becomes ensnared (strength checks to pull them loose). Some of the eldest are walking troves of magical weapons.
Increased leg muscles, quickness- these trolls run almost as fast as stags but have one advantage over them. They can jump 10 times as far as a normal troll. They are almost always found on the surface as those underground tend to hit the ceiling when leaping.
Metamorph- these trolls prey on children. They make themselves look like pets or cute animals and draw the youngsters into their grasp. Fortunately they are still pretty stupid and the wary can detect their presence.
Fear generation, illusion generation- mindbender trolls drive their prey to distraction with fear and bizzare phantom images. Even those who know that they are illusions can be distracted by them because of their alien appearance.
Force grow plants (environmental dependance), drone (variant)- forest trolls rip bits of their flesh off and turn them into a aberration version of plants. Normally these organisms stay small and mostly unseen by all but druids and rangers. If a troll is slain and its blood allowed to soak into the soil, the troll plants grow into monstrous forms that slowly replace the forest around them (or fill the cavern system). Forunately forest fires keep both forms in check.