If you're making a skin for an existing model you don't need to put the .md3 or .wav files in there. All you need is the .skin and .tga files to get smiley to work- Quake 3 already has the actual model, so by including the model and wav files in your zip you're actually creating a whole new mode, and that's something you don't want to do.

Also, one of the .tgas was around 60 times larger than necessary! The tail light need only be 32x32 pixels, not over 2000 like yours was. Making the file larger won't necessarily make the skin sharper/more detailed in game.

If you've got the point release (latest Q3 version) you can pack the skins and bots more easily and leave the /baseq3 folder less cluttered. Instead of editing the main bots.txt file, you can make your own for your particular bot.

I've repacked your skin and fixed everything up- you can download it at http://www.geocities.com/rlyss/q3skn-smiley.zip It's a hell of a lot smaller (only about 150k) rather than your version of over 2MB!
Check out my file and see what I've done for future reference.