Each company does project management a little differently, and that's perfectly understandable given all of the individual concerns and needs that companies are likely to encounter. However, in the experience of Brad Egeland, most companies use a matrix structure (wherein “resources” report to multiple managers), and that matrix organisation is able to standardize processes despite the uniqueness of the organisation as a whole.
As Egeland explains: In a matrix organization, a clear project team is established that crosses organizational boundaries. Thus, team members may come from various departments. A project manager for each project is clearly defined, and projects are managed as separate and focused activities through the use of web-based project management software. The project manager may report to a PMO Director (if a PMO exists), higher-level executive or to one of the functional managers with the most interest in the project.
It is not hard to see where difficulties can arise from this style of organisation: people are interacting with multiple managers, have multiple priorities, and are defined by multiple roles. Because of this, organisations should understand how to balance resources, establish optimized communication, and have a project management office to assure that there is a central control to the enterprise-wide effort.