I make a 3x8 seed stockpile in the middle of my farms, no barrels. No seeds are stored anywhere else.
I make a 2x3 plant stockpile near the farms, no barrels. It feeds a 1x1 quantum plant stockpile, no barrels. This the starting point for plant distribution to all other plant stockpiles. I make a brewable-plant stockpile around the still, a pig tail/rope reed (plus maybe cotton, hemp, etc. now) stockpile around the farmer's workshop that feeds the textile industry, and a quarry bush stockpile by the farmer's workshop that bags quarry bush leaves. (If I get to the point where I feel like doing flour/dye, then there'll be a quernable plant stockpile by the quern, for that stuff.)
I put a food stockpile (allow barrels), which only allows milk, around the farmer's workshop where I do the milking. When I get a bunch of milk barrels, I turn it all into cheese. I put a meat/fat stockpile (allow barrels) around the butcher & tanner workshops, which are always next to each other. The kitchen is close to the meat/fat stockpile. My final food stockpile will be "everything not covered yet, except lye, because you should never EVER stockpile lye", and will be somewhere near the kitchen. Its purpose is to hold ingredients to be cooked (cheese, fish, non-brewable plants, flour, etc.).
I make 6x6 food/booze stockpiles (with barrels) down by the dining room. Sometimes a pure-booze stockpile, and then a pure-prepared-meals stockpile, and repeating when one fills up. Sometimes I just let booze and prepared meals coexist. Very early in the fortress, one of these may also be my "miscellaneous food ingredients" stockpile, but eventually they'll be finished products (prepared meals and booze) only.
I put a leather stockpile (with bins) around the leather workshop, which is typically not too far from the butcher/tanner.
I make a few tiles of thread stockpile by the loom, no bins, just to get thread moved from the trade depot or from the shearing workshop. You can skip that if you don't care about weavers hauling. I make a cloth stockpile (with bins) around the clothier's workshop, because I tend to store a lot of cloth (but very few threads -- I allow auto-looming). The bins in the cloth stockpile cause a lot of job cancellations, but I live with it.
I make a 2x2 stockpile (no bins) which feeds a quantum 1x1 stockpile (no bins) for weapons, for ammo, and for armor. This is especially important for ammo, because you don't want to store ammo in bins (due to a long-standing bug). For armor and weapons, the weight of a bin full of metal implements of death is so great that you do not want them dragging bins of weapons around the fortress. If you don't quantum your weapons, the you need to double-stockpile them (small no-bin stockpile feeding a larger bin-using stockpile, the latter taking from links only). In any case, my weapons, ammo and armor are all stored close to the barracks.
I make a stone stockpile around each mason's shop. Each of these stone stockpiles takes 2 wheelbarrows and only accepts a single type of stone. Thus, each mason's shop deals with a specific, unique type of stone. I make a stone stockpile around the mechanic's shop, also with 2 wheelbarrows, but I don't specify a single type of stone for that. Same for the craft shop that does stone -- any kind will do. I also put my jeweler's shop on the stone level, and it gets a bin-using gem stockpile around it. I don't do much with gems in vanilla, so usually they just sit there.
I make a 2x2 stone stockpile (with 2 wheelbarrows) feeding a 1x1 quantum stone stockpile (no wheelbarrows) by the smelter. These take metal ores, flux and coal stones. Next to that, I make a 2x2 bar stockpile (no bins) feeding a 1x1 quantum bar stockpile (no bins), which gives to the (magma) smelter and to the (magma) forge. These take all metal bars, and coal bars. Having it give back to the smelter is important, so you can make steel, bronze, etc.
I put a wood stockpile around the carpenter's shop, and another around the wood furnace, and a third around the craft shop that does wood. I haven't been using wheelbarrows in wood stockpiles, because it was never necessary in 0.34... but in 0.40, your weaker dwarves haul wood very slowly, so I may change my mind on that. Or maybe just be more selective with who can haul stuff. Haven't quite worked that out yet.
I also don't have a firm system for finished goods yet. It's really, really complex due to all the different types, values, weights, materials.... In some fortresses I have used a quantum stockpile for clothing produced by the clothier's shop (only), with a clothing-refuse-destruction stockpile for any loose clothing. In others I have simply made separate stockpiles for each of the 5 types of clothing ("armor" = upper body, legwear, head, hands, feet) so I can see which one I'm running out of and need to make more of. I haven't come up with a scheme I'm happy with yet.
I generally don't use furniture stockpiles, unless I'm importing anvils to melt. If I do that, then I'll make an anvil stockpile (with 2 or 3 wheelbarrows) down by a magma smelter. I may sometimes make temporary furniture stockpiles for metal furniture near a noble's quarters, with wheelbarrows, in order to get the heavy metal furniture items up from the magma forge to a point near the noble's quarters. Once the statues/tables/etc. have been moved that far by wheelbarrows, it takes less time to build them in the rooms. When that's all done, I'll remove those furniture stockpiles.
The only other time I would have a permanent furniture stockpile (besides the melting anvils) is if I were doing gem encrusting. Which I usually don't.
I never use a refuse stockpile, unless it is really a clothing stockpile with the refuse category enabled to cause disintegration. If there's a goblin corpse or something like that, which I need to move, I will manually dump it.