Were. Doughuts is plural.
Which sentence is correct and why?
1) Doughnuts were the most popular items.
2) Doughnuts was the most popular item.
Doughnuts were the most popular item. (Non-authoritative link to examples.)
The logic is a little tricky. "Doughnuts were" because each doughnut is eaten individually and there is single dish of, say, three doughnuts. "Item", not items, because collectively doughnuts are distinguished from, say, strudels or pastries or chocolates.
Sometimes a dish takes the singular even though it is a plural of nouns, because it is treated as a single object. For example, "scrambled eggs is my favorite".
I think that you could use item or items. I would use were.