Very simple CPU design in LogiSim
Hate to post a "link only" like answer, but I think you should be made aware of Warren Toomey's work with CPU's in Logisim, since it's probably exactly what you are looking for.

He has a couple tutorials building up to a reasonably simple CPU here... 

http://minnie.tuhs.org/CompArch/Tutes/

And if that doesn't float your boat, he has a more sophisticated CPU here...

http://minnie.tuhs.org/Programs/UcodeCPU/

... All of which is well explained, and has downloads to .circ files.



Another great, and arguably more functional, DIY CPU/computer is Magic-1 found at http://www.homebrewcpu.com/. Though it's not done in Logisim, it is quite well documented, including pictures, schematic, description. It is also more than just a CPU in a simulator. It has a ANSI C compiler, an OS, and some software. It's also has the distinct advantage of actually having been built in hardware. In fact, it's currently up and running and serving web pages!



Finally The Elements of Computing Systems and the associated site nand2tetris.org comes in as the #1 recommended information resource for building your own computer from the ground up every time I look into it. Much (All?) content is free of charge I believe. YouTube would agree; many people have made projects starting from this one source.