Cleaning a Disease Ridden Tank

Question
We purchased three green spotted puffer fish from Wal-Mart after doing extensive research on the internet.  We set the tank up as best we could (slightly brackish water), fed them the right foods, and things of the sort.  They were fine for over six months until one-by-one they died.  They looked like they had been squished and them had stuff hanging out of their sides.  Well, it really doesn't matter what was wrong with them as they are dead and we don't have any more.  How should we clean out the tank to avoid infecting new fish with whatever killed the puffers?  It could have just been a puffer-thing, but we don't know.  We think we will go back to freshwater when we get new fish.  Thanks.

Answer
Alright, so you will need to clean the tank with hot water and disinfecting soap. Everything that touched that tank will have to be cleaned thoroughly and air dried before you can even think about putting water in that tank.
So this tank that was before was salt water? If it was, I can not determine the disease but if it is was fresh water than you will have to be more specific on what the "stuff" hanging out of them was. From the sounds of it though you had a parasite that eats the fish from the inside out.
Here is a basic check list for a fresh water tank for the best chance of fish survival:
Proper sized tank
Air pump
Right sized filter (note: if it says it is good for two sizes of tanks, it is best suited for the lowest size. I.E. a filter that does a five or ten gallon tank is meant best for a five gallon tank. A ten gallon is too much for the filter)
Gravel
Reat plants (real plants help reduce nitrates or nitrites)
Hiding place for fish
Light
Something to keep fish from jumping out (algae eaters are famous for this)
Water Conditioner (creates less stress on the fish when topping up the tank or refilling the tank)
Proper Fish Food (my personal favorite is TetraMin Tropical Flakes)
Gravel Cleaner (sucks up the decaying food that has fallen into the gravel)
Catfish (eats food that has fallen to the bottom. Note: the bigger the tank, the more catfish you will need)
Algae Eater (this can be snails, plecos, or algae eaters. Note: While Plecos are excellent choices, they will eat anything that fits in their mouth, including fish)
Heater

The filter will need to be cleaned once every two weeks. The best way to keep bacteria from getting into the tank is little ceramic objects put in the filter (can be found at AquaGiant). The sponge in the filter should also be replaced every now and then.
The gravel should be cleaned once a month to where the water level is about half way down.