Are toilets supposed to be caulked to the floor?
This is a very controversial topic. Some plumbers swear that you must seal the toilet to the floor, while others swear that you should not seal the toilet to the floor.  Some guys never do it, some guys always do it, and some guys only do it depending on the flooring used. It also appears that some toilet manufacturers mention it in the installation instructions, and some do not.

I've heard it mentioned that "it's code" to seal the toilet to the floor, but I've never heard anybody cite the actual code that says it. I'm not well versed in plumbing code, but a quick look didn't reveal any obvious code sections. Though plumbing code (and most other codes), does require you to follow the manufacturer's installation instructions. So if the installation instructions say to do it, then you should do it (if you want a code compliant install).

In my opinion, it's a double edged sword. On the one hand, sealing the toilet can keep water and grime from going under the toilet. At the same time, it also keeps water from coming out from under the toilet.  If you develop a leak, the water will be trapped under the toilet. This could allow the leak to do much more damage, before you notice you have a leak. 

If you flush the toilet and get wet feet, you're going to call a plumber to check the toilet. If after years of flushing the toilet you notice a strange smell, and maybe a water stain on a ceiling somewhere. You're going to start ripping things apart searching for the source of the leak.

To try and alleviate this negative side effect, some plumbers leave a gap in the caulk near the back of the toilet.  While this may let water from a leak out, it also allows water in. Which defeats the purpose of sealing the toilet to the floor in the first place.

If you're installing a toilet in a bathroom where kids are going to be bathing (splashing), it might be worth it to seal the toilet. If you're installing a toilet in a water closet, where there's not likely to be water near the base of the toilet, then maybe it's not worth it. Follow the manufacturer's installation instructions, and use your own judgment.



After doing a bit more research, it does appear that codes require the toilet to be sealed.


  International Plumbing Code 2012
  
  Chapter 4 Fixtures, Faucets and Fixture Fittings
  
  Section 405 Installation of Fixtures
  
  405.5 Water-tight joints. Joints formed where fixtures come in contact with walls or floors shall be sealed. 
  
  Uniform Plumbing Code 2009
  
  Chapter 4 Plumbing Fixtures and Fixture Fittings
  
  Section 407 Installation
  
  407.2 Joints. Where a fixture comes in contact with the wall or floor, the joint between the fixture and the wall or floor shall be made water-tight. 


NOTE: This section may have been moved to 402.2 in 2012 UPC. I did not have access to a copy of the 2012 version to verify.