In all adventures I optimized the npcs in combat encounters, usually by changing stats or giving a bit more hitpoints. Otherwise my experienced players would've had it too easy.
I also used the taint mechanics from Heroes of Horror. Most of the characters got depravity and corruption from Kraken's Cove as it is a severely tainted location (Will/Fort DC 25, 1d3 depravity/corruption). Getting infected by the savage fever also gave 1 point of corruption. The foggy jungle around Demogorgon's temple was also a tainted location giving corruption and failing to resist the wisdom-damaging dreams gave depravity.
The Scarlet Brotherhood became a Riedran organisation and I tried to draw some lines to Sarlona. E.g. one of the characters is from Krezent in Talenta Plains, a serpentblooded human offspring of the feathered yuan-ti who fled from Sarlona (EBCS and Secrets of Xen'drik p.68) and he joined the party to research the history of his people in the Isle of Dread. (Oh yeah, I run STAP in Eberron.)
There Is No Honor
As it is suggested in STAP conversion notes, I turned the cult of Vecna in historians' guild into a cult devoted to Sul Khatesh (one of the imprisoned rajah overlords of Lords of the Dust in Eberron, Dragon 337) and used the One and the Five affiliation from PHB2 (p.176) as a base for it. My CN Illusionist doesn't know what he's dealing with and instead of giving him the normal 'Of the mind' benefit of getting more spells, I gave him a fiendish familiar (from Fiend Folio) that looks like white tiger fur attached to his back. The cult also works as a great background plot, as Sul Khatesh wants to know more about Demogorgon's plans and learn more about the pearl. This gives the character motivation to seek more information as his quests. So far he only knows that the cult has some religious aspect but doesn't care about it and it is knows as the Keepers of Secrets. Maybe later the truth will come out and he'll have to choose if he wants to be a puppet for the Lords of the Dust and gain more power or try to fight back. So far he seems to be slowly sliding to the dark side. I don't know how this all will play out in the big plot but I hope to get some drama out of it. At least my player is greatly enjoying the cult missions and his mysterious (evil) divination and illusion spells that grant him depravity (although he doesn't know this).
I didn't change much but I should've changed the Lotus Dragon hideout as it was a classic and really boring dungeon.
The Bullywug Gambit
Added the corruption effects to Kraken's Cove.
Sea Wyvern’s Wake
I changed the No-Neck fella and his ship into a Riedran ship with sailor-monks and an Inspired shock trooper captain. The characters swiftly rammed and boarded the ship and killed them all.
Changed the animated tower shield (SIGH!) into a large firebrass shield with spearblock ability. (Secrets of Xen'drik and Complete Warrior) Added the notched spear legacy weapon beside the shield. Changed the notched spear's monstrous humanoid bane ability to sacred so it'll be more useful in the later adventures.
Here There Be Monsters
I changed the gargantuan centipedes (=creepy but boring) and mummies to tomb spiders and web mummies (from MM4). It fit the tomb setting much better and I also planned that the shaman's tomb could've worked as a magical location reward (like the touchstones etc) but didn't have the time to work that out. I also don't like the paralyzing fear of the mummies but the sticky web mummies weren't any more entertaining. The first PK almost occured as the druid cast cure serious wounds from prayer beads to the main fighter as he was infected by a tomb spider's negative energy poison. Good times.
I optimized Olangaru with some feats and gave him more interesting magic items. Also, the demonic jungle had a corrupting effect as explained before ^.
Tides of Dread
Not many changes here, but I turned the Olman zombiemasters into potent magical herb-brewing dread necromancers. Devilweed (Book of Vile Darkness p.42) worked as loco weed and I used all the drugs I could find from BoV and Lords of Darkness. The corrupted illusionist is now smoking loco weed all the time and drank juju juice (Terran Brandy p.43, gives +2 CL) in the main battle against Crimson Fleet ships.
Vanthus would've been a pushover for my players so I optimized him to rogue3/fighter4/tempest5. Now they had to flee him and reorganize and attack him again. The yuan-ti sorcerer's flesh golems were dm-polymorphed into serpentflesh golems (Serpent Kingdoms).
Changed the regeneration of fire bats to fast healing as my characters didn't have cold magic.
Changed the mithral breastplate into a serpentskin armor to make it more cool and also allow the druid a possibility to use it.
The Lightless Depths
We haven't played this yet and apart from optimizing the kopru priest of Demogorgon I think I'll only change the elder black pudding into some other, more humane man-eating ooze, like corrupture (ooze) from MM4 or arcane ooze or some other bizarre polyp from Nth dimension.
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Btw, tar pits don't really have tar but asphalt.