SharePoint sites quickly get out of control without good governance

Define policies that force the users to upload only approved types of documents and collaborate with others in the right way, in the right place;
Configure audit at the site collection level to track all the important operations (accessed pages and the frequency, who download, upload, read, delete files and provide summary reports in graphical interface;
Setup good procedures for assigning permissions for users and groups and creating new sites;
Establish life-cycle policies for sites, documents including archiving and destruction requirements and assuring all users are aware about this;
Force the users to avoid keeping irrelevant, outdated documents or other big files (only if it is necessary);
Plan support strategy building a Call Center where thousands of users requests can be prioritize and assign to the right level support (1,2,3);
Create custom site templates based on business requirements and standardize the work for the users. In this way the business and the employees will understand, communicate and collaborate easily minimizing the issues.