Whether and how often to vaccinate your pet is probably the hottest debated issue among veterinarians right now. There is mounting evidence that the annual vaccination schedule that we are all used to may actually be damaging to your pets immune system. Many of the teaching hospitals are changing their vaccination protocols and many vets now recommend rather than vaccinate for everything that their clients pick and choose vaccinating for those disorders for which their pets are at risk.
Current recommendations are that you vaccinate your puppy with a normal vaccination series and rabies. Follow that up at 1 year of age with a booster shot and then revaccinate every 2 to 3 years running titres in between to ensure that your dog has the antibodies for the diseases you wish to protect them from. Then stop vaccinating when the dog is a geriatric dog. Titres tend to be a bit more expensive than the vaccination but if in the long run it's beneficial to your dogs health then you may save more money in the long run.
To determine if your pet is at risk for a certain disease you can talk to your veterinarian, local health departments, and even your own doctor. Lymes vaccine for example isn't necessary for all dogs. But dogs that live in an area where Lymes is prevelent among people are going to be at a much higher risk so vaccinating for the disease may be beneficial to the dog.
Please note that in most areas vaccination for rabies is required by law, and with rabies being transferrable to humans and fatal in almost all cases that to not vaccinate might be placing not only your pet but your entire family at risk.
Here are some links to sites with information on vaccinations, and the immune system.