In my delicious bookmarks:

• http://www.ncbi.nlm.nih.gov/biosystems
• http://www.biocarta.com/genes/index.asp
• http://biocyc.org/
• http://www.wikipathways.org/index.php/WikiPathways

http://www.pathwaycommons.org and of course the commercial players Ingenuity and GeneGo...

I have used KEGG, PID and Panther. You may also check PathGuide: Pathguide contains information about 318 biological pathway resources.

http://pid.nci.nih.gov/index.shtml

Personally I like KEGG Pathways because they provide an XML file related to each graphical representation of the pathway. It gives you the location in x,y coordinates of all the items that are in the pathway. So, with some Ajax and SVG you can easily draw interactive pathways and higlight proteins that match different kind of criteria (e.g. : In this pathway, what are the kinases, Proteases, mutated Proteins or Proteins tested by Western Blot in a given cell lines etc.).

Please find below a screen shot of such a generated SVG file.

It seems that Wikipathways also provide such XML files with each pathway.