For the Chamber of Eyes I did two things. First, I joined the introductory encounter (with the hobgoblins torturing the prisoner) onto the Chamber of Eyes: (i) run the corridor in the introductory encounter onto the entryway into the foyer of the Chamber of Eyes; (ii) add a secret passage exiting the NE corner of the hobgoblin chamber via a secret door and running diagonally, with staircases, up to the balcony in the Chamber of Eyes foyer; (iii) add a spyhole/arrowslit on the E wall of the hobgoblin chamber (near the barrels) looking onto the Chamber of Eyes foyer; (iv) add a portcullis that the hobgoblins can drop in the entryway to their chamber, making the secret passage the only easy path between their chamber and the Chamber of Eyes.
Second, I was prepared to run the introductory encounter, C1, C2 and C4 as a single encounter with waves. The PCs first heard the prisoner being tortured (I made it someone they had already met earlier in the campaign who they knew had been captured by goblins/hobgoblins and were hoping to rescue) and entered that chamber. The portcullis (iv above) was dropped, trapping them in that room. As they made fairly short work of the hobgoblin soldiers the warcaster opened the secret door and fled up the passage (ii above) with half the PCs chasing him while the others finished off the soldiers. The PCs correctly feared that he was going to get reinforcements. The PCs narrowly failed to stop him on the balcony, and he went through the other door and alerted the goblins in C2. I had the bugbear engage the PCs on the upper level, while the skull cleavers came out through the main doors to make missile attacks - some of the PCs jumped down to engage them, while others fought the bugbear and one who had been left behind in the first room attacked through the spyhole (iii above). The warcaster meanwhile went on and alerted the chief, who came forward to join the skullcleavers with his wolf while the archers controlled the long-ish corridor with cover from the shrine doorway (I eliminated the second warcaster as unnecessary).
This was a very dynamic encounter, with PCs moving around through the various corridors in the entry way, going back and forth into the original room to take advantage of the arrowslit, and in the end causing the hobgoblin archers to retreat after defeating the rest of the goblins. (They then took on the archers with the rest of C3 - roused from their drunken revelling - as a separate encounter.)
I also decided that the duergar would wait and see what happened rather than joining in on the potentially losing side of a fight - the PCs discovered the duergar in their rooms as they were looking for somewhere to take their short rest and ended up negotiating a contract with them, paying 300 gp to be delivered in a months time to pay for the release of the slaves (the players preferred this to the thought of having to assault a duergar stronghold).
In the Well of Demons I also ran the gnoll encounters together as a single more dynamic encounter (again leaving the tieflings out of the equation, figuring that they would make a more interesting encounter after the gnolls had been dealt with). The interesting aspects here were (i) the players thought the first chamber with the motely crew of monsters was the more challenging encounter, and so blew quite a few resources on it and therefore were really pushed to the limits with the gnolls, (ii) the use of the connecting tunnel from the boar room to the entry chamber as a way of making the PCs fight on two fronts (and yes, enemies were pushed into the well) and (iii) replacing the barlgura demon with a naldrezu (sp?) from MM2, which is a lurker that captures a PC and teleports it away to munch on it - combined with the two-fronts aspect this introduced extra mobility and tension into the fight.
