Reich UW pages (very useful for nomenclature)
Aldrich Interactive Nomograph (don't distill without it!)
Group Meeting Presentations/Seminars
Leighton (2005-2008 only)
Alex's excellent Chemistry Reference Resolver (how did I live without this?)
A load of classic syntheses are freely available at Synarchive
Jón Njarðarson's 200 best selling drugs poster
Baldwin's Rules at Emory
Useful resources for undergraduate organic chemists (or those teaching) at masterorganicchemistry.com
The chemblog chemistry dictionary for Word (may make your thesis less of a maze of red lines)
Some bits of Organic Reactions are available online for free!
Still open to good stuff I'm not linking! Drop a comment or an email!