Well the first time they do it, they drill small holes in certain areas like under the doors and in the rocker panels. You cant see the plugs normally though you have to get down and open doors and look for them.
Once they have the holes, they spray an oil type product in them and it sticks to the metal. Basically its a rust inhibitor and it repels water so if you have a rust spot thats breaking paint off, this spray will work its way under to where the water is and prevent water from getting into that spot.
It wont stop rust completely but it certainly slows it down and helps prevent rust from eating away other areas.
Since my trucks been done every year since I got it, they take the plugs back out and spray the areas with the product again and replace them. I think it costs anywhere from 100-130 depending on where you go and which shop. Thats Canadian dollars too though.
Heres a link to a shop up here. Theres a bit more info about the product they use and whats involved.
http://www.londonkrownsouth.com/index.html
You can also get small spray cans that I always use to spray certain areas on my truck in between the times I go to the shop and have it sprayed. Its also good for electrical connections so you can pretty much spray it on anything.