Because I prefer the feel of natural fibers over acrylic, I'd probably go with cotton. You can get 1 lb cones of cotton from Joann's, but it is more expensive than acrylic.
Alternately, I'd go with a superwash wool. Knitpicks Bare Superwash in Worsted is fairly cheap, although nowhere near as cheap as acrylic or even cotton. But it does give you the option of knitting up the afghan and if you decide along the way you want a different color, you can dye each panel before you join them, or even dye the entire afghan once it's done.
I also bought wool (not superwash) off ebay for my afghan. I got 60 brand new skeins for about $100. I can make an afghan with half of them and either sell the rest or find another use for them.