I've heard that in some cases toilets are supposed to be caulked to the floor. I replaced both toilets in the condo I moved into last week, and one was calked to the floor, and one was not. One difference was that toilet where caulk was present is on a relatively uneven tile floor, and the one where caulk was not present was on a flat linoleum floor. The instructions the toilet came with made no mention of this.
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.
The actual plumbing seal doesn't have anything to do with caulking around the base of the toilet. That's all to do with the wax (typically) ring where the drain pipe and the toilet fit together, and the bolts that hold the toilet down to the floor.
Caulking around the base will look a little nicer, and it'll keep water and cleaning fluids from seeping under the edge and pooling under the toilet, where they could potentially seep through the floor around the plumbing pipe, or just sit and go stale and stinky. I'd go ahead and caulk the base, but leave a gap in the back so that if a leak develops in the actual plumbing, it will run out on the floor where you can see it and get it fixed before it becomes a bigger problem.
If you use a caulk that sets clear then it would blend in more smoothly, especially if the toilet and floor aren't white. On the other hand, if you some unevenness in the floor that you want to fill with the caulk, maybe you want to find some that sets in a complimentary color.
As a licensed master plumber I would say the answer is in the code, where the fixture comes in contact. 99% of properly installed toilets have a small gap between the finished floor and the toilet base so the fixture is not in contact with the floor. If the toilet is sitting on the tile floor it is likely the plumbing's toilet flange is installed too low, i.e. below the level of the finished floor. Also, if you seal the toilet to the floor with any material, should you EVER have to remove the toilet, you have created a problem with the finished floor / getting the toilet off, let alone if the new toilet base is smaller than the original (visible caulk line left on floor). Also, a properly installed toilet run is sewer gas and water tight from the plumbing stack connection up to the toilet bowl's rim so the only water that should be on the floor is from a person, floor cleaning water, floor rinse water, or worst case is a blocked: stack, toilet pipe or waterway and the resulting overflow.
I've worked in construction in the past. I also understand the double standard on this topic. As of now I work as a realtor and have recently had a home inspection point out sealing the toilet to tile as necessary repair. On a personal note it works both ways. If you have a 2nd story bathroom that the tub floods in its going to seep through your first floor ceiling (whether you've sea led the toilet or not). Baseboards at the floor most likely are not sealed. I would rather leave the toilet unsealed so I could determine where the water is coming from. First floor I would absolutely leave it unsealed otherwise you wouldn't know about a leak until it was too late (especially on a slab).
After reading all these posts, I believe the magic answer for me is to fill in my 5/16" floor gap with a round foam seal for sealing window gaps. It's temporary, but looks nicer than the gap at the floor. It also keeps out dirt but will let some water out in the event of a leaking wax seal, especially if a gap is left at the rear. If it starts looking grungy, I'll pull it out and put a new piece in...should take less than 5 minutes.
Many previous responses here bring up good points, but one thing was not mentioned. As a do-it-yourself-er who has installed and uninstalled many toilets over the years, I have learned that it depends. On a tile floor, I prefer sealing the base with silicone (not caulk), because sometimes it is not possible to tighten the bolts just enough for the toilet not to move all so slightly without breaking a tile. If there is a small amount of movement, the wax seal can develop a leak over time. By glueing the toilet in place with silicone, it is guaranteed to not move. I do leave a gap in the back. It is not difficult to cut through the silicone seal with a knife if the toilet has to be removed (and to remove any residual silicone from the tile floor with a scraper after removal).
This has to do with a sanitary aspect of plumbing. a wax ring seals the drain and the caulk seals the fixture to the floor covering the gap. where pee pee and pooh pooh will be trapped unable to be cleaned and cause a unsafe condition.
caulking a toilet is in the plumbing code it says it right there in black and white, the argument that it "could be talking about the wax seal,is BS" if it was addressing the fixture connection it would also address the glue and solder for the drain pipes on the other fixtures.
my credentials master plumber in 3 states, superintendent for a mechanical plumbing co. 34 years experience. CAULK THE TOILET !!!