Reading and Theory
Music Theory
MusicTheory.net - Theory, ear training and note identification games. Also apps for iOS devices.
Theory Time - Graded workbook series for kindergarten through high school. Examples are piano-based, but still useful for guitarists.
Reading Material
Read This First - Great text to introduce sight reading for guitar.
Sight Reading Factory - customize-able, randomly generated sight reading samples (subscription required).
The Guitar School - Free music for guitar solo and ensembles.
Forrest Guitar Ensembles - Free music for solo and ensemble, helpful grading system shows general difficulty level of various works.
Delcamp Scores for Classical Guitar - Lots of free guitar scores listed by composer, also runs a popular classical guitar forum.
Petrucci Music Library - Archive of sheet music for all instruments, virtually infinite resource. Can be a bit difficult to navigate unless you know specifically what you are looking for.