To move a project to the top of 'Your Projects' list, you'll pin the project. To get started, go to your Waffle Dashboard by clicking the Waffle icon in the top left corner. Here, you'll see all of the GitHub repos you have access to that boards already have been created for.
To choose which repos you want to see at the top of your list, click the push pin icon of that particular repo to move it to the top of 'Your Projects' list. The push pin of a 'pinned' board will be purple. If you have multiple repos pinned, they'll be in alphabetical order at the top of the list, followed by the rest of the repos which are also in alphabetical order.