I've been doing some pondering and arithmetic in my head thinking about the following question:
What would it take to create a "Closed Loop Farm"?
A "Closed Loop Farm" is one which can remain in continual operation without any external inputs. Everything it uses it produces itself and no non-renewable resources are consumed. In short, this is "permaculture". Some allowances must be made for the use of stone and metal in the initial setup to create the infrastructure, but it is important that these resources not be consumed. Similarly, hunting and foraging are acceptable for obtaining initial materials and plant samples, but the end goal is that the only things you use are those which you have grown on your own land.
Basic Currency
And this brings us to the fundamental calculations for how the "cost" of items, and how to balance production and consumption of the fundamental driving resource: Humus. Humus humus humus. In a Closed-Loop farm, "Humus" is the currency for all things. Fields cost Humus, gardening pots guzzle Humus, your only abundant fertilizer will be Humus, and thanks to the miracle of Forestry, even WOOD can be expressed in terms of Humus. You like humus right?
Humus Production
It is clear that to do anything valuable or interesting, Humus will be required in VAST QUANTITIES. This leads to the most important question that must be answered: What is the most efficient way to produce large quantities of Humus? (I will do some rounding and estimations here, but will generally stick to the lower estimates of a given range.)
Sources: Due to the restrictions of this challenge, there are only 3 sources of Humus: Trees, Potted Plants, and Field Crops.
Trees: Trees are a time-consuming, labor-intensive low-yield source of Humus. You would be a fool to fill your compost bind with woodchips. However, for the sake of completeness, I will give a brief analysis:
Any Tree:
-Yield: 66 Humus
A felled tree yields 60 Wood Blocks, and destroying the stump gives another 6 blocks (sometimes 5, but 6 is more convenient). 66 Wood blocks = 132 Woodchips = 66 Humus.
-Cost: 6 Humus
Assuming your proficiencies are high enough to have at least a 50% success-rate from planting cuttings (so that tree farming is sustainable), it will take roughly 2 pots per tree, which is a total cost of 6 Humus. It also takes a long-ass time to "Harvest" a tree; Fell it, Chop it, Chip it.
-Profit: 60 Humus
-Time: 10 Days
3 days to sprout the saplings, 7 days to grow the tree.
Rate: 6 Humus per Day per tree (and the dedication of 2 pots)
This means, interestingly enough, that you can have a Tree-Only farm, with nothing else providing your Humus, just diverting about 10% of your lumber production to provide sustainable humus. Depending on the rate at which cuttings grow back on trees, you can have a sustainable tree farm with less than 50% sapling success. It will just take 3 pots per tree instead of 2, raising the Humus-cost to 9.
Potted Plants: I will assume that you have the indispensable skill Horticulture, which gives you a profit of 2 plants per pot, instead of just one. Even with that nearly all pot-able plants give just 1 humus per unit, which isn't enough humus to refill the pot and replant it, never mind the need to make a profit. All the plants except...
Baby Bears: The tiny pumpkin that cares!
-Yield: 5.2 Humus
2 Baby bears when sliced yield 4 pumpkin flesh and 12 seeds.
Update: Unsliced Baby Bears also give 2.6 humus each, so slicing is not necessary.
-Cost: 3 Humus
-Profit: 2.2 Humus
-Time: 3 Days
Rate: 0.7 Humus per Day per pot
For Pot-Only farming, for every 2 pots you have growing regular crops, you will need 3 growing Baby Bears to provide the Humus. This means that only 40% of your pots will be "Productive", the remaining 60% needing to be dedicated to Humus production. Not terribly efficient, but somewhat less hassle than Woodchips.
Field Crops: These are where it becomes practical and relatively hands-off to produce large quantities of Humus. Not all crops are created equal though. For my calculations, I am going to assume that through a combination of your Stocks&Cultivars bonus, and the use of 1 Humus for fertilizer to boost the plenty (will be factored into total cost), the pessimistic average Plenty value will be 125%: 15 from the humus, 10 from S&C. Actual values may be higher than this. Although some crops may yield an increased profit from a 2nd (or even a 3rd Humus), for the sake of uniformity, I will stick to just one.
Cereal: I have seen comments that this is a good Humus source for when you go large scale. Let's do the math!
-Yield: 10 Humus
125% plenty = 125 seeds. 25 Are used to replant, and so 100 go into the Compost Bin for 10 Humus.
-Cost: 3 Humus
2 to prepare the field, 1 as fertilizer. Woodchip cost is ignored as it is negligible and well below the margin of error.
-Profit: 7 Humus
-Time: 3 Days
Rate: 2.3 Humus per Day per Field.
4 fields (yielding 13.3 humus per day) will exceed the production capacity of a single Compost Bin (12 per day).
Update: Although the humus yield is low, Cereal is the best choice for high purity compost, which is much more valuable than bulk stuff. Also, Hay is apparently quite valuable, potentially outweighing the value of humus produced.
Corn: The yields are terrible, but I include this here for the sake of completeness.
-Yield: 3.7 Humus
125% plenty = 62 seeds. With 25 used for replanting, leaving 37 left to make 3.7 Humus.
-Cost: 3 Humus
The yield from corn is so low, that the +15% plenty from 1 humus ferilizer gives only raises the yield by 0.7 Humus, resulting in a net loss in its application.
-Profit: 0.7 Humus
If no fertilizer were applied, the profit would be 1 Humus. Still pathetically low.
-Time: 4 Days
The longer growing time hurts Corn even further.
Rate: 0.17 Humus per Day per Field
The 0.25 per day you'd get without the wasteful fertilizing is still pathetic. Would not recommend.
Cotton: I've never tried composting cotton (fresh or cleaned), so I will calculate based on composting its seeds only. Will update if I learn differently.
-Yield: 3.7 Humus
62 seeds minus 25 for replanting = 37
-Cost: 3 Humus
Just like corn, fertilizer is wasted.
-Profit: 0.7 Humus
-Time: 4 Days
Rate: 0.17 Humus per Day per Field
With seeds only, cotton works out to be just as bad as corn, except that you can make cloth. Terrible humus source.
Cabbage: Its seeds take a while to dry, but I will assume that there are seeds in stockpile allowing for immediate replanting and composting of extra.
-Yield:16.3 Humus
125% = 5 heads which are split into 6 leaves which give 0.5 humus each. 30 leaves * 0.5 Humus = 15 Humus. 13 excess seeds are left after planting which can be composted.
-Cost: 3 Humus
-Profit: 13.3 Humus
A second humus as fertilizer would give a slight profit if it produced an extra 3 leaves instead of only +2.
-Time: 3 days
Rate: 4.4 Humus per Field per Day
This is nearly DOUBLE the humus profit than you get with Cereal. If you're using Cereal for humus, you're a chump. 3 fields of cabbage will exceed the production capacity of 1 Compost bin. 1 bin per 2 fields recommended. Cabbage with 2 fertilizers will exceed even that capacity, which might not be worth it for small profit.
Pumpkins Grows slow, but that serves to reduce its effective humus cost.
-Yield: 35 Humus

125% plenty = 5 pumpkins. Each pumpkin gives 6 pumpkin flesh and 15 seeds. Total of 30 flesh and 75 seeds, 25 of which are replanted. Each pumpkin flesh gives 1 Humus, and the 50 seeds give 5 more. 35 Humus.
Update: Pumpkins can be placed directly in the compost without slicing, and yield the same amount of Humus. Slicing is only necessary for replanting, which reduces the overall bother somewhat of harvesting.
-Cost: 3 Humus
-Profit: 32 Humus
Could actually profitably take a 2nd and 3rd fertilization. If fertilization pushes it past a 25% increment, then you get an extra pumpkin. No matter how deficient in flesh that pumpkin is, it still gives 15 seeds, for a guaranteed 1.5 Humus. The point at which fertilization is no longer profitable will depend heavily on whether it nets you an additional pumpkin or not, but in terms of just the flesh, anything below +5% plenty is wasted.
-Time: 6 days
That's kind of a long time, but the yield more than makes up for it.
Rate: 5.4 per Field per Day

This is the best Humus production rate of any of the crops, hands down. Pumpkin flesh is produced in similar quantities to Cabbage leaves, has double the potency, but takes twice the time, balancing out. However, the pumpkin seeds boost pumpkin's overall yield by 25% compared to cabbage, and the fact that all costs are effectively halved by its less frequent need for field prepping helps too. Pumpkins are by far the most effective farmable source of Humus in the game. Given their large but infrequent (a bin processes a full input in 4 days) but large yields (2 fields fills 3 bins), to ensure smooth production of humus with a minimum of Bins, you will either need to stagger the harvest times of your pumpkins or hold some in reserve to top-up bins that were previously full.
Pumkin2Win:
The results are clear. For both Potted Plants and Field Crops, the Pumpkin is the winner for producing large quantities for compostable material.
Other Considerations:
I ignored a few complications in my prior calculations:
Hay: I didn't mention that Cereal produces Hay, which is worth another +2 compost. This is because even with that boost, cereal still lags behind Cabbage and Pumpkins in productivity, but most importantly it's too valuable to get chucked in a bin and rot.
Also Hay-related is that an alternate source of Hay to growing cereal is growing Autumn grass in pots. However, 5 pots will yield just 2 Hay and cost 15 Humus to produce. Growing a field of Cereal will take only a little bit longer, cost less Humus to plant, and yield a useful product. Don't bother potting grass.
Charcoal: Charcoal is a renewable resource too! If I even bothered mentioning Trees as a source of Humus, but I didn't talk about putting them to proper use as charcoal. Shame!
It's because I was lazy and you probably didn't want to read a re-analysis of the humus yields with the application of Charcoal. I'll just give a rough estimate that using 3 Charcoal instead of 1 Humus for fertilizer will raise your Humus rates by about 50%. Pumpkins still win. The "Humus Cost" of charcoal is fairly low, around 0.05 Humus per piece. (1 tree gives a minimum of 120 charcoal and costs 6 humus to sprout. You do the math.)
Turkey poop!Yes it's a source of compost, but I don't think you'll make any profit off of feeding turkeys and composting their poop. It does allow for meat-production in the "Closed Loop Farm", which is handy, but not relevant to the production of Humus. (unless you drop turkey cuts into the bin, but I still don't think it's worthwhile or even profitable)
Mining! Yes, it's something which is "harvested from your own land", but it's technically not renewable, and most importantly: you can't make Humus from it! Dross won't help your humus production one whit. You can however inefficiently smelt high-purity Iron using locally grown, organic, sustainably harvested charcoal (ya damn hippy), and use this as the source of your nails, but no iron products get regularly consumed by farming, so it's not really relevant.
I have a Lime quarry on my property! Ok, that is a locally produced resource, but while abundant, it's not infinite. Besides, do you really think it's worthwhile to convert Lime into Humus? Sure you can get a good conversion rate by boosting pumpkins (1st lime gives about +10 Humus), but isn't Lime best used for smelting bulk Iron to defend your compound? I suppose if you've walled-in your quarry then you can use your Lime however you please, but not everybody has that luxury. Anyways, I digress.
My S&C level gives me WAY better yields than that paltry 10 or 25% you're calculating with! My estimates were based on pessimism. Pessimism is reliable. If you get higher crop yields than what I calculated, then good for you! You'll need more compost bins, the low-value crops will be proportionally more effective, and Pumpkins will STILL be top dog. Grow Pumpkins. PUUUMPKIIIINS!!!
TL;DR:
Pumpkins are the best crop for making large quantities Humus.