Best Practices for Eclipse's Problems View
I feel that filtering "On selected element and its children" is the best mode of Problems view filter, because it allows you to very quickly narrow down the scope of reported problems: click on Working Set (in Package Explorer), and it shows all problems in all projects in the set; click on a project - and only problems in the selected project appear. Click on individual class (or package) - only problems in the selected class (or package) are shown. So you don't get distracted with problems unrelated to your task at hand.
In the top right hand corner of the problems pane is a filter button (it looks like three arrows pointing to the right), clicking that will let you configure the view. You can filter by element, such as the class you're editing or working set, the type of problem (e.g. java problems, buildfile problems etc..) and by severity. It's actually very configurable.
See http://help.eclipse.org/help32/index.jsp?topic=/org.eclipse.platform.doc.user/concepts/cprbview.htm for details and screenshots.
To view more than 100 warnings, go to the problem view's drop down menu (use the little arrow next to the minimize button on the view), select Preferences, and you will have the option to change this limit from 100 to another number.
This information is for Ganymede; things have changed since Europa and I'm not sure of all the differences.