You will have to be more specific. There are many different ways you could use Alfresco to manage documents involved in a stage-gate process. For example:
Do you want to organize the files according to stages? Or just use a status field that denotes the stage the document is in?
Do you want to try to automate some of the review and approval using an Activiti business process or do you want to handle that external to Alfresco?
Do you need Alfresco to gather the documents that are ready for review for a particular gate? Or is that not a requirement?
Do you need to remind users when they are missing approved documents that are required to pass through a gate or will that be handled elsewhere?
Some people will use Alfresco as an "enhanced" file server and nothing more. The documents are part of a stage-gate process but the system doesn't really know anything about it. Others will add some or all of the above features. It's really up to you and the business to decide.
The most of my interests is how to organize the bundle of files according to stages. What I can imagine is to bundle the related files/folders in a folder and hold it with metadata that represents stage. In this case the number of holding bundle folders will increase with number of stages and it's difficult for users to track change of a file between bundle folders. Is there any good ideas?