Analytical Resources

Spectral database of organic compounds - analytical data of simple compounds  
Sigma-Aldrich - analytical data available for most commercially available compounds, MSDS
University of Cambridge optical rotation calculator

Journals & Literature Databases

JACS Journals - search JACS, JOC, Organic Letters, etc.
El Sevier ScienceDirect - search Tetrahedron, Tetrahedron Letters, etc.
Google Scholar 
Organic Syntheses - search for reliable procedures
RSC Journals - search Journal of the Chemical Society, Perkins Transactions, etc.
Thieme Connect - search Synthesis, Synlett, etc.
Web of Science 
Wiley Interscience - search Angew. Chemie Int. Ed., European Journal of Organic Chemistry, etc.

Other Databases 

Bordwell pK_a tables - extensive pK_a data
E-compound - database filled with compound information, mechanisms, and more
Oxford University chemical and safety information - MSDS and more
Synthetic Pages - user-added synthetic procedures
University of Edinburgh Azeotrope Databank - heterogenous and homogeneous

Techniques & Tips

Not Voodoo - tips and tricks from other grad students
Chem Know How - message board 
Stoltz Lab Forum - message board 

Freeware

Bio-Rad KnowItAll - for drawing chemical structures
ACD ChemSketch - for drawing chemical structures

Brain Teasers

Princeton's Organic Mechanisms Club - organic chemistry exercises under "problems"
Dave Evans' Challenging Problems in Chemistry and Chemical Biology - database of problems, keys available
Fukuyama's Group Page - problems sets from group meetings with keys