The available information on produce is fairly sparse. Let's fix that!
Anyone who has checked my numbers on this feel free to concur or correct and I'll try to adjust the main posts accordingly.

NOTE: NOT YET UPDATED FOR CURRENT VERSION!

I am assuming the listed water cost is 'per game-hour' and not anything else.

Agricultural bugs: There are a lot of them. They include output not properly showing up in storage, storage reporting full when it isn't, crops being stuck in one state or another, scientists never tending to the crops or being stuck tending to them, and harvests just vanishing.
A reload will usually fix most of these but can sometimes introduce others. Overall, the system does limp along well enough to support your crew with occasional reloads.
The worst agriculture bug currently is ⁠suppliers removing the second biomass they bring rather than leaving it for a future harvest, which is effectively tripling the time crops spend idle (exception: algae) and will greatly reduce your yields from their theoretical maximums.

General agriculture information:
A crop won't call for a scientist until it is fully grown, which can add a lot of wasted time depending on where that scientist is. However, the game does seem good at queueing multiple jobs to a nearby scientist rather than giving the nearby scientist one planting job then calling for the next closest halfway across the ship.
All crops (excluding coffee and tea) have a 5 minute planting time and a 5 minute harvesting time if nothing is bugged.
It is not yet clear if crops will draw water continuously or as an up-front cost, or if they will still draw any water when grown but unharvested. There is conflicting information on the 'standing crops' like corn and oranges but agreement that crops that have water in their visuals (algae, peas, etc) are draining water each hour. If water is drawn each hour, we don't know if it's reduced proportionally for growth cycles that don't complete on the hour.

The water cost of the biomass used to grow a crop is not included in the water/cost rates.
The planting and harvest times are factored in to maximum outputs.

Algae is the only crop that produces biomass instead of consuming it.
Since it doesn't need to be restocked with biomass, the same scientist that harvests the crop will usually replant it immediately. Algae therefore has the closest actual output to theoretical output of any crop.
It does mean algae is the only one likely to see this visual bug: plots will report 'no output storage space' and seem nonfunctional until a harvest has been picked up. However, they are growing and the GUI will snap to the current position in their growth cycle once the harvest is taken away.

Additional: On paper, peas are hands-down the best basic crop and superior to both aeroponic options due to their incredibly short growth time. However, the way the growth and harvest process currently works hits them harder than any other crop because of that short growth cycle, so their actual output isn't quite as nice as it seems.
On the other hand, because they grow so fast they can sometimes be harvested and replanted before a supply officer shows up to cart away the second biomass, which puts their output right back up again if you keep your supply division busy.
The great weakness of the pea is high biomass usage, with one algae crop sustaining just over 1 1/3 pea crop in continuous production.

Beans are a terrible investment, with the worst ratios in both time and water usage.
They currently have a bug causing their 'double harvest' to only make 1 additional produce, meaning they're even worse than the maximum output would indicate

The only crop that grows slower with a grow light. Don't grow them in the same room as higher-level crops, or they'll be nearly as bad as beans.

Less crops per hour but also less biomass per hour.
A grow light makes wheat produce more per hour than even the mighty pea, but wheat still has slightly inferior water efficiency.

Very slightly superior to wheat in water and time usage, has a decent edge in biomass used with a grow light.

About the same output as the tier 2 crops or mushrooms without grow lights. Not actually more water efficient than wheat or rice unless you're not using grow lights

Like the bean crop, the 'double harvest' of tomatoes doesn't actually deliver, giving only 5 produce instead of 6. At least here it's 2/3 the listed bonus instead of 1/2.
I'd swear I did the math wrong on something here, but it stayed the same when I double-checked. If someone gets better numbers let me know!

A great crop without a grow light, excellent with one.
Unfortunately inferior to oranges, so build those unless you're a chronically unlucky soul and wouldn't receive the doubled harvest as often as you should.

Unlike the other two doubled harvest crops, the orange double harvest performs as advertised
Because the double harvest completely fills the internal storage, it's the only crop that can't be restocked with biomass before at least some of the harvest is removed.
This means that oranges typically need to make 4 calls for a crewmember instead of three, their sole deficiency compared to corn. The average amount of time this adds and whether it means corn tends to be more productive per hour has not been determined yet.