I'm just wondering which level(s) of Doom feel(s) the most "cryptic" for you. I know the term "cryptic" is very vague, but can't think of any other word.
The Ultimate Doom:
- E2M4: this one holds for me the first place in the list of cryptic levels in every Doom version. I think it's a mix of many things: the eerie music, the strange layout, the odd secrets it has, etc. It just feels cryptic, like you just can't understand what's going on. Every time I play it I can feel that, no matter what, there are a lot of things about this level that I'll never get to know.
- E4M1: the NIN secret. 'Nuff said.
- E4M4: just... WTF!? This level has always felt out of place for me.
- The Chasm: it isn't that much cryptic, but it has one of the most cryptic secrets I've ever seen: I've always wondered what was Sandy thinking about when he made that useless invulnerability sphere secret.
I think that's all for me. You can add of course levels from the Final Doom to the list; I didn't just because I'm not that familiar with those WADs.