It depends. Saplings give the most per item, but aren't the easiest thing to farm, and give you a lot of waste products if they're the only thing you're looking for (though there's plenty you can do with wood, of course). Wheat could work, since you can ferment wheat directly and also turn seeds into plantballs. Cactus and sugarcane seem like good options (sugarcane more than cactus, probably), and they have no waste products to worry about.
Does anyone use mushrooms? They seem like they'd be the hardest to collect automatically, though maybe you could do something with a mooshroom spawning/shearing machine. Now that I mention it, I may have to try that just for novelty...