Milestones and labels serve as efficient tools for organizing issues, but prioritizing tasks can be enhanced by reordering issues and pull requests to reflect their importance. By utilizing a drag-and-drop feature or keyboard commands, users can rearrange issues within a milestone to highlight which tasks should be addressed first. This system allows teams to visually prioritize their workflow and focus on the most critical issues. Additional information on milestones and issue prioritization can be found in the help guide authored by Ayman Nadeem.