gammadragon: The Even More Incredible Machine release by gog.com allows bypassing of the copy protection, but the screen still appears asking for three parts appearing on a manual page. I've found a way to completely remove the copy protection so that the game no longer prompts you to check the manual.

The gog.com TIM.EXE file is 114652 bytes and is compressed and encrypted twice over by an old app called "PRO-PACK v2.08" (PP.EXE). The first encryption key is 0x1993 and second is 0xFFFF (or the other way around, if you are encrypting).

First step is to unpack the executable twice, then run the file using a debugger and find out how to patch the EXE to remove the copy protection. I've done this with my own unpacked TIM.EXE file.

Unfortunately, I haven't found out how to patch the original gog.com executable yet in order to remove the copy protection. But I can provide the unpacked executable and the patched version with copy protection removed:
http://www.patchery.net/files/tim_unp.zip

To apply this, just backup your original TIM.EXE, download the zip file and extract it to your game directory, overwriting the existing file.

NOTE: It's generally a bad idea to obtain random executable files from the internet and run them, so think carefully about this before you actually download and apply it.

If anyone has any thoughts on how to further improve this, I'm open to ideas.