[Sextante][1] is a geoprocessing library that can be used from several GIS applications. I recommend you to use it from [gvSIG][2] as i think that it has the best integration. Sextante also allows (if you configure it properly) use algorithms from SAGA and GRASS.

Here you can see [a video that shows how the modeler works][3].

Update: From March, [qgis also has a Sextante plugin][4] that works really well.


  [1]: http://sextantegis.com/
  [2]: http://www.gvsig.org/web/plugins/downloads/gvsig-1-11-portable
  [3]: http://www.youtube.com/watch?v=zvm_zV9nr3U&list=UUhxDtM3siarv_3l5I9_UMxA&index=24&feature=plcp
  [4]: http://plugins.qgis.org/plugins/sextante/