Pretty much everywhere - but in an organized way.
I keep the cats stuff in "her" room - food, water, litterbox, treats, toys, everything. There's a little organizer/drawer thing, too. The birds stuff is on the bottom shelf of their cage.
Dry dog food is in the hallway closet. Supplements and open bags of treats are in a cupboard in the kitchen. I keep three or four cans at a time in the kitchen as well. I keep raw in the downstairs chest freezer, and move a weeks worth at a time to the upstairs freezer. In the spare room, I have an organizer that has unopened bags of treats, chews, toys, canned food, etc - I'm a bit of a stockpiler.
And then of course, toys, beds, and leashes are just laying around all over the house.