RaTcHeT302: I've made a few more fixes and I added them to the main patch, the folder structure is different. It really bothered me how the Do Not Touch animation always glitched out but it works fine now. Also the intros are disabled, I'm not sure why you added that Video folder back as it's reduntant.
http://community.pcgamingwiki.com/files/file/404-evil-genius-pcgamingwiki-patch/

I am also working on a gameplay patch but it's part of a separate download.
http://www.nexusmods.com/evilgenius/mods/7/

Bear in mind that I'll keep releasing fixes for the first patch just in case, the version number is there just for the looks though.

The gameplay patch does have a 200 pop cap and whatever else other features. There are quite a few changes although I can't be bothered to list all of them right now.

I don't know if any other animations glitch out, the DNT trap was the only trap I could think of.

This Mega Patch is kinda outdated already, seeing as it might be missing some of the newer files, along with some other changes.

dm3588: You're recommending two patches here, the one on pcgamingwiki and the one on nexus. Since they're both made by you, are they compatible? If so, which one should be installed first?

RaTcHeT302: Use only one, either pick the PCGamingWiki patch for fixes only, or the mod for fixes + gameplay changes.

The mod includes the fixes I made from the patch already, so only use one.

Either way you might need to merge some stuff manually if other mods use the same files from the patch.