One challenge that we have at my place of employment is figuring out the best way to centralize our Reporting Services code.  We have many customers and each customer has their own database but most of the reports that we develop for customers are the same.  So what we have done is to create a separate folder called DOLM (Deploy Once Link Many).  What we do within this folder is locate our base reports.  From this folder we create and push out linked reports to customer's database folders. 

What is the great part about this technique is that we maintain one set of centralized reports and push out these reports to the customers folders.  Withing the customer folder the report name can be changed and the default parameters can be changed depending on the customer. 

So, if you haven't even considered using linked reports I recommend that you definitely look into them!