The exercise I use most for improving tone is long tones.  I use the same routine that is in Mark Van Cleaves' Maximizing Practice Vol 1. This is a great routine, that is perfect for working on tone, delivery of air, and ease of production.  It basically starts with warming on low C using expanding intervals.  You play Low C with a full sound,
crescendo and decrescendo.  Then, move to low B, and repeat.  Then C#, Bb, D, A, Eb, etc.. down to low F# to F# on the first space.

After this, you do the same routine but start on G in the staff, expanding your way to low F#, and G above the staff...

This routine has worked very well for me and my students...

- -Donovan-