Due to character limits, I had to add a second factory tutorial post.
To make each factory work, no matter which one you have, you must first click on the processing gears (the wheel looking things between the scale & the water faucet on the task bar), then click on the product you want to harvest for the factory.
If you click on the scale in your task bar, then on the new screen click buildings, then click factories, you can hover over each factory to see what it processes.
The Factories & What They Process (items highlighted in gold have the highest profit margin):
Oil Press & Tuscany Oil Press - sunflowers, olive trees
Perfume Factory (both styles) - Lilies, red roses, morning glory, daffodils, forget-me-not, lavender, chrysanthemums, carnation gold, pink roses, white roses, lilac, black roses
Pickles Factory (red & Russian style) - eggplant, cucumbers, red peppers, yellow peppers, cabbage, green peas, marrow, zuchinni, turnips, white turnips, pattypan squash
Pillows Factory - peacock, dodo bird, rooster, goose, egret, mallard, swan, black swan, pelican, flamingo, holiday dodo, Valentine's swan
Popcorn Factory - corn
Potions Factory - amanita, aurelia, barracuda, corpse flower, ginseng, iguana, phoenix, rattlesnake
Syrop Factory (blue & Russian style) - green maple tree, red maple tree, yellow maple tree, birch tree
Spices Factory - onions, red onions, red peppers, garlic, crocus sativus, crocus luteus
Sugar Factory - sugar beets, sugar cane
Tea Factory - jasmine, tea bush, tea rose
Tequila Factory - agave
Weaver Loom & Tuscany Weaving Mill - flax, cotton, holiday camel, holiday polar bear, white rabbit, Tibetian yak, black sheep, white sheep, rabbit, horse, deer, unicorn, pegasus, wild ram, ghost sheep, ghost horse, camel, polar bear, reindeer, rudolph, Valentine's polar bear, Valentine's sheep, Valentine's rabbit, groundhog
Winery & Tuscany Winery - pomegrante tree and grapes