Anti-teleportation zones: like already mentioned zones of great power block teleport. Basically irrelevant at low levels, quite the game changer at higher levels.
Ossra:Page 150 of serpent kingdoms has basically a poison gas clouds, they also buff serpent folk instead of damaging them.
Permanent spells: Permancy allows you to stick a wide variety of spells on an area forever. Altough it only works with some spells, it still offers a wide variety.
Planar traits: From Manual of the Planes, altough normally present on other planes, they can “spill” on other places trough portals and whatnot. They can empower, maximize, block or disrupt sertain kinds of spells depending on alignment and magic schools. A large selection of them available, many times will benefit some kind of magic while hindering another. Or boost everything up or down. Or make stuff fly. Lots to choose from.
Stronghold builder's guide: This book could be said to be dedicated mostly to this aspect. Includes LOTS of nice stuff including how to use exotic materials, mobile fortresses, traps and plenty of other nice stuff. If you have it, definetely check it out. Below are two sections that I specially like.
Wall Augmentations: from Stronghold builder's guide, those allow you to add special effects to walls, like granting SR/cover to those nearby, or hurting those nearby with blades/fire/poison or blocking special ways of travel.
Wondrous Architecture: Also from Stronghold builder's guide, these are basically a collection of large wondrous items that can't be equiped but can be put in an area. Of course, nobody says you can't fit them in a closed chariot/floating plataform and have it transported around. Those that stand out more are
-Brazier of Bright bursts, low DC, but area blindness activated by word and also raises the alarm is pretty nice.
-Cabinet of stasis is a no-save no-anything you-lose effect, as long as team monster finds a way to make a player enter it. And it tecnically isn't a trap so the rogue can't even search for it. Very evil. Very nice.
-Chamber of climbing grants spider climb to everybody inside. Cheap way of increasing minion mobility.
-Chamber of the Earthbound supresses most magical flying. Get back on the ground and fight like a man batman!
-Chamber of guidance is dirt cheap and grants a +1 bonus on a single roll for those who know the command word.
-Chamber of Hidden Character supresses alignment detections, more usefull for team monster than you may think.
-Chamber of seeing ends invisibility effects. Stop sneaking around Batman!
-Chamber of sloth causes slow on those who enter. Keep team monster out and lure the party in somehow.
-Chamber of speed gives haste to those inside. Keep the party out and keep the monsters in shooting ranged attacks.
-Chamber of the unliving is basically a permanencied Antilife Shell.
-Cloudgathering orb messes the weather around the area.
-Desecrated Shrine is a large area Desecrate.
-Engraved Circle of Protection(Alignment) is a permanent Magic Circle of Protection.
-Guardian Statue is a nice way to rise the alarm.
-Hall of Bable messes up the ability to speak, wich can be devastating against batman.
-Hall of (insert spell name here) come in diferent styles replicating diferent spells.
-Hole of Hiding is a permanent Rope trick, pretty usefull for hiding ambushers.
-Hurricane's eye creates a permanent Hurricane around an area. Available in weaker wind forms.
-Inscriptions of concealment hides non-living stuff from all divinations. And also vision. A must have for powerfull undead organizations.
-Inscriptions of Falsehood blocks scrying and normal vision, but allows a Will save for the second.
-Inscription of Privacy just blocks scrying, but it's considerably cheaper.
-Platform of Jaunting is basically a mini-teleport pad. The greater version has unlimited range.
-Platform of Healing uses Heal on anyone steping on it. Perfect for hit and runs.
-Plataform of telekinesis. Remember those floating rooms I mentioned? Here they are. Fit them with cover and siege engines for improvised airships.
-Prison of (insert element here): rooms whose walls, ceiling and floor are covered in dangerous magic stuff. The prismatic version allows for the creator to go trough safely. For the others, find a way to give your monsters immunity so they can safely pass.
-Secure chamber grants mindblank to all those inside. No Batman you can't mindrape the king or his advisors on his own throne room.
-Sigils of anti-magic is your basic dead magic zone, replicating an AMF inside.
-Sigils of Supression duplicate the always usefull Globe of Invulnerability, wich stops new spells of 4th level of lower from having effect but doesn't supresses ones already in existence. Also available in lesser version.
-Touchstone of Faith gives a deflection bonus to one creature standing over it.
-Tree of Jaunting looks like a normal tree, but replicates Tree Stride on any who enter it. Available in greater version.
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Tainted locations: From Heroes of Horror, some places are so evil they slowly corrupt you by themselves by giving you taint, wich then inflicts all kind of penalties. Better suited for darker campaigns If you're using them however, make sure to ban tained scholar Prc, wich is very very easily abused.
Dread Effects: Also from Heroes of Horror, a bunch of dark evil area effects. Bloodgrass hinders healing, bloodstones increase the critical threat range of everybody in the area, and charnel bog disrupts good and healing spellcasting, make characters wake up fatigued from rest and can also inflict diseases trough the air. Finally Night Stone simply deals negative energy damage around it (hint:undeads are healed by negative energy damage).
Haunted Locations: Continuing the trend from Heroes of Horror, undeads can attach themselves to a location for a variety of nasty effects, including keeping to come back if destroyed, making stuff move by itself, illusions and some others.
Frostburn: This supplement gives out rules on a series of cold-related hazards, from simply extreme cold weather dealing cold damage, to chances of thin ice breaking, hypothermia, thawning, flash floods and several other hazards expected in cold enviroments. Sleet, slow blindness, plenty of effects to challenge the party. Aurora polaris in particular deals a whooping 20d6 electrecity damage to everybody in the area! If your campaign is in a cold region, definetely check this out! Even if it's not in a cold region, heck, you can get some other reason to mess up with the weather in a region to use this rules.
Dire Weather: Also from Frostburn. As the party levels up and starts to be easily able to ignore the mundane weather problems, throw them this ones!
-Acid sleet and Razor sleet deal bigger damage.
-Bloodsnow deals Con damage.
-Death Hail deals Str and Con damage
-Howl of the North are even nastier winds
-Negation Flurry dispels stuff.
-Rust Flurry destroys equipment.
And several of them can leave patches of magic snow that replicate those effects even after the dire weather calmed down.
Magical Terrain: More nice stuff from Frostburn,
-Ebony Ice boosts undeads.
-Faery Frost dazes people.
- Lighting Pillars shoot lighting bolts to anybody nearby.
-Snow Geysers randomly explode dealing damage to those nearby.
-Also fields of bloodsnow, negation flurry and Rust Flurry.
Supernatural Manifestation: yet more stuff From Frostburn, Coldfire is a liquid that doesn't give a damn about gravity, meaning you can totally make walls of it, or all kind of nasty traps. It deals coldfire damage that can't be healed in cold regions. Also snowflake lichen looks like snow and deals cold and Dex damage depending on how close the party is.
Frostburn terrain: This book enviroment section ends up with diferent kinds of terrain, but what really stands out here are skybergs. Floating icebergs. Just think of the possibilities!
Sandstorm: The counterpart from Frostburn, Sandstorm focuses on hot enviroments. Heatstrokes, hot enviroments, dehydration, all the kind of stuff you expect when you go into a desert, volcano or plane of fire. If your campaign is going ttrough this kind of terrain, you want to check out this book.
Sandstorm Waste Hazards: Like Frostburn, the mundane hazards of Sandstorm are easily countered by medium-high level players, so time to throw the bigger guns!
-Black sand sucks light creating darkness and deals negative energy damage.
-A Devil Dune is a mountain of sand that moves on it's own to cover up people and is pretty hard to stop.
-Flamestorm is literally a rain of fire.
-Flaywinds deal damage, and can be combined with Black sand for even more lethal effects.
-Furnace wind deals fire damage togheter with wind effects, and furnace zones simply deal fire damage whitout save.
-Leech salt makes creature get dehydrated that much faster (altough easily countered by a flask of endless water).
-Mirror sand makes people blinded just by trying to make spot/search checks.
-Moondust suffocates people unless they have a specific counter.
-Plains of glass are harder to travel by, and release showers of shards when nearby explosions happen.
-Red sea is liquid salt that deal the nasty dessication damage to both creatures and metal equipment.
-Slipsand is a quicksand in steroids.
-Slumber sand makes people asleep just by going over it.
-Wailing Waste makes creature on the area go insane.
Stormwrack: The third book of the “enviroment” series, Stormwrack focuses on water campaigns. Honestly I have little experience with this one as I mostly do adventures on dry land, but if you like this kind of stuff, definetely check it out as it has plenty of cool water-related stuff! Also gunpowder siege weapons as already mentioned.