A Pilot's Reference

AOPA Online
+ http://www.aopa.org
Home of the Airplane Owners and Pilots Association. A comprehensive site for General Aviation.
NavMonster
+
http://www.navmonster.com
A dandy pre-flight site, free and open to the public. IFR pilots covet the TripKit feature.
DUAT: Weather and Flight Planning Service
+ https://www.duat.com
Prints perfect kneeboard-sized flight logs.
SkyVector Aeronautical Charts
+ http://skyvector.com
For the visual planner who hates to fold charts.
Digital Airport/Facilities Directory
+ http://aeronav.faa.gov/index.asp?
xml=aeronav/applications/d_afd

Updated every 56 days; download the PDFs to your e-reader, or print as you go.
NOAA METARs and TAFs
+ http://adds.aviationweather.gov/tafs/index.php
The source for current and forecasst weather.
NOAA Winds Aloft
+ http://aviationweather.gov/products/nws/winds
National winds, depicted in multiple formats.
AirNet Winds Aloft
+
http://www.usairnet.com/cgi-bin/Winds/Aloft.cgi
A visual depiction of winds aloft, and in MPH.
  Federal Aviation Administration
+
http://www.faa.gov
The mothership. All the documentation, explanation, and regulation you will ever need.
AirNav Aviation Information

+ http://www.airnav.com
Good for intel on airports and FBOs.
100LL.com
+
http://www.100ll.com/
Avgas pricing, by the region, by the airport.
VOR Simulator

+ http://www.relia.net/~george/aviation/sim
Some visual context for VOR readings.
Flight Planner Enroute Charts
+ http://www.fltplan.com/LogOnToCharts.htm
Charting based on airport IDs, with weather too.
Mississippi Navaids
+ http://www.fltplan.com/Nav/State/MS.htm
The scuttle on local VORs, NDBs, etc.
Exams for Pilots
+ http://www.exams4pilots.org
A study site for bad weather days.
AVweb News
+ http://www.avweb.com
Aviation news and professional site.
Salon's Ask the Pilot
+ http://dir.salon.com/topics/ask_the_pilot/
Trade column by airline pilot, Patrick Smith.