You can use lists in any template query, or in queries you create yourself in the QueryBuilder.
Search the list of all template queries for "homolog":
and select the Template "Find computed homologs":
The template query can use an existing list instead of an identifier.
Click the checkbox to select a list, and run the query:
The results table shows the zebrafish genes from the list with homologs in mouse, human, and fly:
You can create new lists from results tables. Click on the "List" button for an expanded menu:
(adapted from the FlyMine Manual)