I've got an article titled "Advanced Matrix Reporting" over at Simple-Talk that was just published.
The biggest issue I find with the Matrix control in SSRS is the difficulty in doing complex aggregates other than SUM. Sometimes you'd like to do variances of year over year totals. Check out the article for dynamic dataset creation, query based grouping, dynamic column names, cells-in-cells technique, custom matrix aggregates using InScope() and custom chart coloring.
Check it out here:
http://www.simple-talk.com/sql/sql-server-2005/advanced-matrix-reporting-techniques/