OS/2 Executables

Has anyone ever looked at the linker script for Hexen or Heretic? They are linked as OS/2 Linear Executables, and I'm pretty sure the same must have been done for DOOM and Strife. But the question is, why would iD do that?

Because the DOS Extender they used probably needed this format.

They used DOS/4GW, and WatcomC, both had a seperate format for 32 bit DOS programs (I've tried it myself)

The Watcom 32-bit extenders use the LE file format attached to a DOS stub. Just because it was developed for OS/2 first doesn't mean it isn't used elsewhere.

Yup. When you want to load any of the EXEs into IDA Pro, you gotta tear off the DOS extender first in a hex editor because IDA, despite containing a large amount of DOS-relevant knowledge including what all the interrupt functions and IO ports do, doesn't know about the concept of extenders. Just gotta snip-snip at the second MZ header inside the file :)