6" Manufactured Chimney system or 8"??

I would wait to decide on the chimney until after you have the stove decided. Spend the time getting your wood pile in order and figuring out which stove to put in there.

With that said, I believe most (but certainly not all) current EPA stoves use 6" chimney. However, some of the larger ones (for example the Blaze King King) use 8". So I'll turn the question around on you - what are you looking at for a stove? Other than your signature indicating you want to keep heating bills down, do you have other objectives and parameters you need to stay within? I.e. significant other with interior design ideas that may preclude a particular stove style?

How large is your home? How about the room you plan to place it in? Is the floor plan well suited for heating by wood stove or might you be a better candidate for a wood fired furnace?

Unnecessary repetition of what slow1 said:

Most modern stoves have six inch flues, but I would wait until you have that decided.

the cost difference from 6 to 8 is enough to make you pick a 6" stove. 99% of the modern stoves are 6".

But the big stoves are generally 8". So the question remains, do you want a big stove that will heat a large area and/or have long burn times, or are you looking for a small to med/lg stove?

If the used stoves you are looking at are not EPA rated, you should really reconsider...

the oversized stove's are eight inch. Plenty of 6" stoves have the capacity to heat a large area and have long burn times. I would never sell a 8" stove to someone that did not already have a 8" chimney, the cost is just to high to justify. IF you buy a used stove that is 8", i think thats a mistake. The cost difference between 6" and 8" will almost buy a stove, and most certainly buy a Englander or a quad millennium. Down the road, when that 8" stove burns out, i wonder if there will even be any more 8" stoves. I can only think of 3 8" stoves on the market, out of hudreds of models.

Once again, the OP can buy a new stove with the cost savings between a 8" flue and a 6" on a three story house. I think installing a 8" flue for a used stove is a serious mistake. I bet that 6" system will cost in the neighborhood of $2200. I bet the 8" system would be in the neighborhood of $3300. I will have to work it out when i get to work.

ok, i built both systems to be sure i was giving decent advice. The 6" with 28' of pipe turns out to be $2377 (ICC chimney). The 8" was $3645 (ICC) . Thats a $1268 dollar difference. That goes along way to purchase a new quad 5700 step top, or any stove for that matter. Factor in the 30% tax credit, this would make buying a 8" used smoke dragon out of the question.

You got me convinced MSG

Now the only counter-argument would be if that 3 story house has a need for a very large stove that requires an 8" pipe eh? But then again, at that price difference it might be better to get two stoves with 6" pipes - one on the first floor and one on the second eh?

the 5700 is a huge heater for a 6" chimney
http://www.quadrafire.com/Products/Wood_Burning/Wood_Model.asp?f=5700
Specifications
Heating Capacity: up to 3,500 sq. ft. †
Maximum Log Length: 24”
Firebox Capacity: 3.44 cubic feet
EPA Certified: 4.13 grams/hour
Efficiency: 76%
Weight (body only): 515 lbs.

but... its so easy to forget that stoves are zone heaters, not whole home heaters