The Same Handy Chemistry Links (unorganized, though explained)

http://cirrus.chem.plu.edu/
An undergraduate chemistry research database from Pacific Lutheran University.

http://www.chemicalelements.com/ and http://www.webelements.com/
Two interesting periodic table sites. All you ever wanted to know about the elements, and more.

http://www.organicworldwide.net/
A comprehensive set of organic chemistry tools, from lab techniques to structure analysis.

http://www.liv.ac.uk/chemistry/links/reactions.html
http://themerckindex.cambridgesoft.com/TheMerckIndex/NameReactions/TOC.asp
Two compendia of name reactions; each has great references but no mechanisms.

http://www.aist.go.jp/RIODB/SDBS/menu-e.html
A Japanese government website with an excellent spectral database.

http://www.cem.msu.edu/~reusch/OrgPage/tables.htm
Data tables for solvents, NMR, isotopes, and other topics from Michigan State University.

http://www.chem.wisc.edu/areas/reich/pkatable/index.htm
Very thorough lists of pKa’s in DMSO.

http://www.mdlchime.com/chime/
Free Download of a chemical visualization tool.

http://www.organiclinks.net/
Where are the synthetic organic chemists in the USA?  Here's a pretty comprehensive list!

http://dgr.rints.com/
A searchable database of the ACS Directory of Graduate Research

http://www.rsc.org/chemistryworld/news/2007/april/23040701.asp
The Hirsh index -- a measure of scientific importance measuring publications and citations