Christina,
Something successful I have been using is Weighted Scoring Model as method for project prioritization. In this you can identify key parameters and assigned weights to different criteria (e.g., ROI – 30%, Strategic alignment – 30 %, Technical Complexity 40%, etc.)
For any new project coming will then score each against these criteria as cross functional team helps derive prioritization index which further used as managing projects.
In terms for online tools, there are few which know such as Smartsheet or Wrike as they offer project prioritization templates, which can be helpful to start with as a reference. Also, you can refer to ProjectManagement.com which includes a wealth of templates and resources for different scoring and prioritization models.
However, as pointed by Kiron above - as no two companies will have the same plans/constraints so above can be for reference. Hope this helps..!!