NOTE: Much of the following was confirmed by looking in the JK.EXE itself.
Only 32 lights can be "on" at one time. Note that the player usually is one, and a weapon's muzzle flash is one, and each weapon projectile is one. If more than 32 lights are created, others will start to turn "off."
A level made in JED may contain no more than 640 things. JK, however, needs space for spawned things as well, making a level with 640 3DOs on startup crash. JK supports 640 things, both dynamic/spawned and static 3DOs.
If more than 127 adjoins are visible in JK, the engine will show HOM at those adjoins beyond the first 127.
Very large limit on number of meshes. (The limit is based on the maximum value of an integer and available memory.)
There is a limit to how many resources (.3do, .key, .spr, etc) that JK can load. It seems to depend on how big the files are, however, the latest from Sige is that JK does indeed load everything into memory, but there's only a certain amount that JK will keep track of (kind of like the thing limit). If you remove res2.gob and replace it with the 'bare essentials' (which are unknown to the writer of this section at this time) you can load more resources than if you had the original res2.gob in resource. Also, JK must be able to run without the CD, as JK will load res2.gob resources off of it.
Setting too many surfaces in one sector to extra light 1 seems to mess up the 3do lighting. (Changing some of the walls back to extra light 0 solves the problem.)
Only 32 translucent surfaces can be in view at once. Those beyond the 32 will be completely see-through (i.e. not showing the texture at all).