[Anthony]

Looking over I Smell A Rat... (spoilers follow)

My first reaction to 'rats in a cellar leading to a deeper dungeon' is 'ugh, done that'. It's pretty much a cliche at this point. Going on from that:
The Cellar
Other than genre conventions, I don't see why PCs wouldn't just come in, kill the spiders, collect the heads, and be done. My experience is that PCs aren't going to bother spending multiple hours digging through dirt unless they have a pretty good idea there's something valuable or important behind it, and a door does not by itself qualify. Also, the rest of the adventure is reliant on the PCs fully illuminating the cellar (which they might not do) and making a roll.

As an encounter, seems fine.
Twisting Tunnel
Not a fan of "roll for random damage that's probably going to bounce anyway". Plus, given the way you get into the tunnel, the PCs have appropriate tools and are obviously in no hurry.
The Sewers
Once again, why are the PCs doing this? Also, again, the rest of the adventure is dependent on a single skill roll.
Smugglers' Den
More random stuff unconnected to the adventure concept.
Rune-Limned Gallery
There's no interesting challenge here, just automatic damage. I guess it's a way to prevent the PCs from clearing a room, returning to rest, etc, but there's less heavy handed ways of doing that.
Ritual Chamber
The Peshkali should have some dialog lines. This seems like a perfect opportunity to invite the PCs into the service of evil (presumably this invitation will fail, resulting in combat, but this thing is a guardian, not an ambusher).

This seems like a good point to remind the GM of the Recognition rules on Monsters p4, as this fight can't be won until someone figures out chopping off the arms (which they might do anyway -- if you can't kill it, disarm it -- but a hint would be very useful).

The challenges in this fight don't make much sense. Why doesn't the Peshkali tear down the false wall as soon as it becomes evident that the PCs are a threat? Or just command the zombies to come out and help?

The evil altar should have DR and HP (though it should also attempt to curse people who attack it); "blow it up" is a default delver response to anything weird.
Hidden Tomb
No comments other than the above.
Main Hallway, Cells
Why are monsters (that are on the same side as the bad guys) behind locked doors? They should probably trigger and come out when PCs do something. Also, the antimagic paint is interesting enough but doesn't seem to be relevant.
Library
The black book should be on the map. Also, there's a chance PCs will snipe the book from the hallway (a fireball would do nicely) in which case presumably the contents of the room will mostly survive.
Lab
I would expect players to try and do something about the cloud of poison, not just go bumbling about collecting alchemical supplies, and if they do decide to scrounge, that seems like a perfect time for the toxifier to attack.
Testing Area
The challenge in the testing area doesn't seem related to anything.
Blasted Passage
Is there a need to make the encounters here random?
End of the Line
This fight probably won't reach -HPx10 unless the PCs have overwhelming firepower, since Merle only has an 18- base consciousness roll. As boss fights go, it seems... boring.