Since resurrecting of topics is okay on this forum per the rules as long as I have something to say (which I do), here are some more addons with secret levels and the levels they are off of (in general, I am not posting for mods by authors that appear to still be highly active on this forum, in case they want the courtesy of not having the information spread; also I'm mentioning original Wolf3D/SoD sets only if they contain secret level(s) that are NOT accessed from the normal floors):
The Golden Episodes (Arielus):
There is one secret level in each episode, accessed from: E1L1,E2L2,E3L3,E4L1,E5L2,E6L3 (basically 1,2,3,1,2,3 interesting pattern)
Rising Evil and Rising Evil II: Double Trouble (Haasboy Software):
Not sure if the first has any secret levels. In the Double Trouble the first secret exit is on Floor 4. Haven't memorized any others.
Chemical Warfare (Jack Ryerson):
(Thomas asked about this one in an earlier post also.) There are 5 secret levels and they can be reached from levels 5, 10, 19, 24, and 33.
The Renovation (BJ Rowan):
Normal secret exits except in Episode 4. In that episode the 10th floor is boss and the 9th is secret. The normal elevator from Floor 8 takes you straight to Floor 10; the secret elevator leads you to Floor 9. Floor 9 has an elevator that ultimately takes you to Floor 10. Episode 5, while having a secret exit on the normal floor (Floor 5), also has a very hard and tedious to find secret exit on Floor 1. If you find (and use) it, you will skip Floors 2 through 5.
Renovation II: Conflict in the Fatherland (BJ Rowan):
In episode 1 there is no secret exit on the normal Floor 1. Instead, BJ played a little trick and the episode has 4 secret levels, 3 secret and 1 super-secret. It starts on Floor 6, where you can leave the episode without a boss fight. However there is an exit hidden on this level that takes you to Floor 7. If you go there you must play up through Floor 9, where you have another chance to leave without a boss fight. However the map hides another exit, which takes you to Floor 10, the real and legitimate boss floor of the episode, if you find it. All 5 other episodes have normal secret exit levels.
Temporary Insanity (Nat):
Very old (yet classic) 3-episode set. The first and third episodes have some special secret exit positions. In E1 you have a secret exit on Floor 1 to Floor 10 as usual, but you also end the episode at Floor 7 if you don't find a secret that takes you to Floor 8, which exits to Floor 9, effectively rendering Floors 8 and 9 as secret. In Episode 3, the secret levels can be reached from Floor 6, rather than 7 (you cannot play all 10 levels of this episode, because if you use the secret exit on Floor 6 you skip Floor 7).
Wolfen60 (very old set by various):
Normal except Episode 6, which is a straight 10-map episode (no secret levels of any form).
Two secret levels, they are off of Floors 4 and 15.
Nazis With Attitute (Michael Collin):
Also two secret levels, they are accessed from Floors 1 and 12.
Schabbs 2000 (Gary Ragland):
There is one secret level, Floor 9, off of Floor 8. The normal exit from Floor 8 leads to Floor 10.
Countdown to Disaster (Gary Ragland):
Two secret levels, they are reached from Floors 2 and 11.
I might have more to add to this list later but this should hopefully have added a lot of mods where secret exits are not in normal positions. I hope anyone interested finds this helpful.