In no particular order:
Jed Wentz Bach: Complete Sonatas for Flute (Performed on period instruments. Jed Wentz is a true artist. Even if you’ve heard a million versions of Bach’s flute music before, make sure you listen to this CD because it will blow you away.)
Tadeu Coelho 18th Century Flute Sonatas (I love the energy and brilliance in this CD. One of the few recordings that almost seem to have a “live” concert feel.)
Emmanuel Pahud Paris (This is a new classic. A must have collection of French flute music played beautifully.)
Various Artists Flute Greatest Hits (Very affordable collection of single movements and whole pieces performed by great musicians. A good intro to flute music for everyone.)
Jeanne Baxtresser Orchestral Excerpts for Flute (A companion to Baxtresser’s book: Orchestral Excerpts for Flute
Required reading and listening for all serious flutists.)
Various Artists Flute Passion (An amazing collection of some of the most important compositions for flute: Bach to Berio, Schumann, Reich and others in between.)
Ian Clarke within… (A CD of fantastic compositions by the flutist and composer. It has great cross-over appeal. I highly recommend it!)
…more to be added for sure!