If you can get the mindset that "quantity" actually means "units" it should be no problem.
Examples:
Apples are $0.59 per pound (I'm picking prices out of the air. I have no idea the real price.)
Cantelopes are $1.98 each
You simply set the prices at $0.59 and $1.98 respectively.
To order 6# of apples and 3 cantelopes the customer would enter a quantity of 6 for apples and a quantity of 3 for cantelopes. The total price would add up correctly.
However, this leaves a somewhat confusing display on the product page. It's going to be up to you to clearly indicate what a unit is on the product page.
For instance a statement in the apples product description might be "Priced per pound" and the statement on the Cantelope page would be "Priced per cantelope".
You may want to replace "qty" in the "add to cart" box to "units" and then in the product description state "units = pounds", "order by units...1 unit equals one pound" or similar verbage.
To change the wording in the add to cart box open /includes/languages/[your_template_name]/english.php and enter new text for define
HTML Code:
('PRODUCTS_ORDER_QTY_TEXT','your custom text here');
On the product lists it's going to be a bit harder to indicate what a unit is. Before the latest version 1.3.9h of Zencart I was using an add-on in the downloads section called: Short Description (not the one titled "Short Description for Categories"). I'm not sure if it will work with Zencart version 1.3.9h but off hand can't think of any reason why not.
This add-on provides another short field or column on the product lists for supplemental information to be displayed. The information also appears on the product description pages. So you could put the statements mentioned above into this field so that "Priced per pound" shows up both on the product list and the product description pages.