Generally I use Iodophor for bottling, & Star-San for everything else.
I keep a spray bottle of Star-San solution (prepared with distilled water) hanging in the kegerator. It's great to be able to spray my keg posts, QDs, and faucets when I'm swapping kegs. It's also great to have on hand when an airlock pops loose or gets gunked up from blowoff--I can just rinse it in the sink with hot water, then spray it down with Star-San solution, and I never have to go through the hassle of mixing up solution "to order" for these little unforeseen projects. If you use distilled or RO water when you prepare it, it lasts over a year (BTDT, checked with pH paper) in solution.
I also use it to clean/sanitize cutting boards, knives, grinder parts, etc. when I'm butchering pigs in a barn that has no running water.
For bottling, I use the "Vinator" spray sanitizer gadget that sits on top of the bottling tree. Star-San foams too much when you are blasting it into 50 bottles in rapid succession. And I worry that it might make the corks too slick when I'm bottling wine. In these cases, it's Iodophor all the way.
Another thing Iodophor has going for it is that while it may stain your soft plastic stuff yellowish, it won't make hoses all gummy and gross if you leave them sitting in the solution overnight. Star-San produces some sort of slime on plastic and makes soft vinyl sticky if you soak it for several hours. Fortunately, there's really no need to soak anything for more than a second or two with Star-San. Just wet it, remove it, and 30 seconds later it's ready to use.
If I had to choose only one sanitizer I guess it would be Star-San, but Iodophor is superior in some cases, so I keep both on hand.
