As reported on the related idea (https://community.hubspot.com/t5/HubSpot-Ideas/Folders-to-organize-Workflows/idi-p/11319/page/10#com...) you can now organize your workflows into folders on the workflows listing page. Navigate to the workflows tool and you’ll see an updated design for the Workflows listing page. There's a new option to “Create folder” in the top right. Once you create the folder, you can bulk select workflows and move them into the folder.
Note: You can only create one level of folders, and cannot nest them. Deleting a folder also deletes all the workflows inside of it, which is made clear in the prompt.