ModelBuilder is not the most fashionable part of the Geoprocessing Framework since the advent of ArcPy but it still plays a key role for those who want to visualise their processes in a way that code alone cannot.  Coupled with enhancement of the much maligned background geoprocessing progress bar (which seems to be Under Consideration for improvement) is enough for me to rank it #3.

• Inactivate (“comment out”) a tool in ModelBuilder
• Add Previous/Next extent buttons to ModelBuilder for easier Navigation
• Add Find tool to ModelBuilder (also expressed as Find Option in Model Builder Edit Mode and Search A Tool in Model)
• Geoprocessing progress in background needs better indicator

PS I almost included “Save As” in Model Builder here but am pleased to note that this was implemented in 10.1 – thanks Esri!