gmo Editor is a generic level editor for indie game developers who use Windows. It also happens to be free and open source. The editor is built to be reconfigurable, so you can set it up to work well for your game project.
Ogmo saves your levels as XML files, which will play nice with most programming languages and engines. C# (XNA) and ActionScript3 (Flash), for example, both have superb built-in XML support.