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Another way of referring to a ZC quest. The only difference is that "custom quest" refers to any quest file that is not hard-coded into the Zelda Classic player. Effectively, the only quests that cannot be termed "custom quests" are the files 1st.qst, 2nd.qst, 3rd.qst, and 4th.qst. (3rd.qst and 4th.qst are technically fan-made custom quests, but as they are official Zelda Classic quests, the program treats them the same as 1st.qst and 2nd.qst.)
The "custom" description is a relic from the days when Zelda Classic was solely intended for creating "Xth quests" and alterations to the original Legend of Zelda First Quest and Second Quest. These days, the sheer variety of game types that can be found in custom quests is so broad that the term is usually shortened to just "quest."