If your pet is on a maintenance dose of a prescription, you can ask for the prescription from your vet and get it filled at most pharmacies including Target, Walgreens, Costco and Sam's Club. (Even non-members can use the Costo or Sam's pharmacies although payment options may be limited to cash and cetain credit cards.) This includes some pet-only meds as well as those for humans too. Like anything, you should shop around. My experience is that Costco's prices are among the lowest and typically significantly lower than Walgreens. Still, even Walgreens might be cheaper than some vets. Consumer Reports said in its August 2011 issue that vets' markup for some scripts is 100 to 160 percent.
I also found Costco's prices much cheaper on Greenies Pill Pockets than any local retailer ($4.30 for 45 each or 1.6 oz.). Find them behind the pharmacy counter at Costco. PetSmart was asking $7 for the same item. Amazon.com charges $6 including shipping. If you can get your cat or dog to swallow the pill by simply coating it in butter or sticking it in a piece of bread, good for you.
Here's another pet product that can get expensive--Feliway. If anyone's vet recommended Feliway diffusers and spray to reduce anxiety in cats/dogs, save a lot of money ordering them online. I have found the cheapest prices at Entirely Pets. If you order $85 or more, shipping is free.
Consumer Reports also found that the cheapest prices on pet foods were at Wal-Mart, followed in order of cheapest to more expensive: Target, Petsmart and Petco.