they have more health and stuff...
The different pipes were originally mostly added to give variety to recipes, but then people wanted to be able to place them in the world too. I tried to make them different with different capacities on some pipes, but large pipes just slow down the flow, and small pipes cause sloshing, so in the end I set them all to the same size.
Basically, the only real difference is longer underground pipes, just use whatever material you have more of, or whatever colour you prefer.