Pets and Vaccinations – Helpful or Harmful?

I have had pets most of my adult life. We have laws that require us to vaccinate our pets. Our veterinarians remind us yearly that our pets are coming due again for these vaccinations. I have now had two very bad experiences with pets and vaccinations. One was years ago and it cost my cat his life. One is on-going right now with my puppy, Buffy, currently, and suddenly after having her second set of vaccinations at just 12 weeks of age became lame, had a fever, with all four paws swollen – diagnosis – Hypertrophic Osteodystrophy (HOD). In Buffy’s case it is highly suspected, even by my Vet, that Buffy’s HOD is a reaction to her last set of vaccinations. Are vaccinations, as recommended by most vets helpful or harmful?