Classical Guitar
ThisIsClassicalGuitar.com
This site is owned and run by Bradford Werner of Victoria, BC, Canada and is a great resource for classical guitarists.
Jazz Guitar
LearnJazzStandards.com
This site offers excellent tutorials and backing tracks.
JazzGuitar.be
Though much of the site is in promotion of the paid material, the blog section offers a lot of great free lessons.
Rock Guitar
TroyGrady.com
I would be hard pressed to find a person who has done more investigating on they playing styles of pick players than Troy Grady and his series Cracking the Code. There are many videos that he offers for free and the payed content is WELL worth it.
Music Theory
MusicTheory.net
Strengthen your music theory skills with written and aural exercises.
Teoria.com
Teoria is another good theory resource with tutorials, theory and ear-training exercises, articles and more.
Ukulele
UkuWorld.com
This is a powerhouse of resources for ukulele – chord and scale generators, an online tuner, chord charts and tab sheets for many songs, and guides and lessons on all things uke.