I'll respond on Quickbooks and TurboTax since I'm familiar with that combination.

Quickbooks allows you to identify each account to the Sch F, etc.  It also flows seamlessly into TurboTax.  You will need to enter your Depr. items into Turbo Tax as you have each year.  Quickbooks allows you to setup your Capital purchases as "Fixed Items" and then they can be tracked thereafter.  You can tie in additions to a purchase, i.e. the new roof on the barn, or the new engine in the tractor, or if you want to keep a running total of the setup costs, etc.

I use a seperate account for each piece of real estate in the Chart of Accounts to track my basis for the initial purchase and any additions that are depreciable.  I add the additions as sub-accounts to the initial account for each farm, for instance.  This can be done for any item that you want to track. I just don't use individual accounts for machinery, just an account for Trucks, one for Trailers, another for Machinery, etc.  Then I track each individual item by class tracking.

You can use "class tracking" in QB for many different scenarios and you can set up jobs to tie expenses together with too.  I use the inventory feature to track my products on hand which is valuable to me in dividing expenses between different enterprises and entities.  QB allows me to accomplish accrual and cash accounting that I can understand and benefit from.

With the newer releases the last few years (I've been using it for 10+ years I think) the reporting features have expanded greatly, almost infinately.  I also like being able to invoice my sales to customers with a customized (by me) invoice.  I can pull it out of inventory and it is priced or I can override the price if need be.  The real value of QB for me is the ability to customize it to my needs, however creative I feel.  And yes, it can be taught what a bushel or acre is just fine.  While a farmer doesn't need inventory tracking for tax purposes, it sure is handy for many other reasons, especially if your are trying to maintain an inventory of filters, etc. for the equipment.  I buy the stuff and then invoice it to the machine when it is used.  I have mine set up with bar codeing too and use it with a wireless scanner in the shop.  Neat, huh?  You can bar code it in and out the same way.  Open the bag and scan in the stuff, then scan it as you use it.  Then I can print a report of the items I need to order to make sure the inventory is kept in stock.  My practice is to do that whenever I choose before going to town or placing an order.

I don't try to tie all of my overhead expenses to each enterprise, because in reality, I will own the pickup whether I plant a field or not.  It figures into my total expense before profit is determined.  I used to do that with Farmworks, i.e. fly the helicopter over all of my fields, but I have loosened up on that kind of stuff.  I try to track the actual items that affect the profit of an enterprise, and leave the overhead expenses that are going to be there anyway, such as insurance, etc. to appear on my P/L statement.  The idea is to have enough profit in the total collective dollars from the various enterprises to offset the overhead and living expenses.  Then you have what I like to refer to as PROFIT!!!