FAA reference materials:
Pilot's Handbook of Aeronautical Knowledge
Airplane Flying Handbook
Instrument Flying Handbook
Instrument Procedures Handbook
Aerodynamics for Naval Aviators
Aeronautical Information Manual (HTML)
Aviation Instructor's Handbook
Aviation Weather Handbook
Risk Management Handbook
Tips on Mountain Flying
Weight and Balance Handbook
ATC 7110
FAA Airman Certification Standards (PPL, IRA, CPL)
FAA Practical Test Standards (CFI)
Awesome ground school/learning resources:
Bold Method
The Finer Points Online Ground School
Sporty's Online Training
PilotSafety.org
FAA WINGS Program
Weather resources:
AviationWeather.gov
Pivotal Weather (models)
Online charts:
SkyVector
Aeronautical Chart User's Guide
Digital Chart Supplement
Minimum Vectoring Altitudes and Minimum IFR Altitudes
Electronic Flight Bags:
Foreflight
Garmin Pilot
Podcasts:
Jason Miller's The Finer Points Podcast
Opposing Bases
Ask the A&Ps
Aviation News Talk Podcast
VSL Aviation Podcast