Hello every one:

I believe everyone knows some valuable websites and everyone keeps looking for some more. Why not we just post here what we know pool all of them here?

Here are three seed links. If you find them useful please keep posting yours.

Protocols:
http://www.protocol-online.org/
https://catalog.invitrogen.com/index.cfm?fuseaction=iProtocol.home

Free online software or free online analysis
Sequence or structrure analysis
http://kr.expasy.org/
http://bioinformatics.org/sms/rev_comp.html

Restriction ANALYSIS
http://tools.neb.com/NEBcutter2/index.php
http://www.neb.com/nebecomm/EnzymeFinder.asp

Primer design for Mutagenesis
http://www.invitrogen.com/content.cfm?pageid=9716&CID=KNC-GOOGLE&s_kwcid=pcr%20primer%20design|527216593
http://bioinformatics.org/primerx/cgi-bin/DNA_1.cgi

Secondary antibody selection guide:
http://www.piercenet.com/products/browse.cfm?fldID=7C4CFD31-5FF6-42CA-8E00-437E8A42B8FC

Biotinylation reagent selection guide:
http://www.piercenet.com/products/browse.cfm?fldID=48842E1D-F817-4EFD-AC41-75959543B030

Crosslinker selection guide:
http://www.piercenet.com/products/browse.cfm?fldID=26436A16-60A0-4A56-85F7-213A50830440

Free antibody technical handbook:
http://www.piercenet.com/Objects/View.cfm?Type=Page&ID=61E3C646-3EEA-47DD-A9AF-1DB253C7EAB6

Here's a resource for finding general information about all sorts of things . . . not just science:
http://www.refdesk.com/

These sites are very helpful.

Don't forget SS protocol site:

http://www.scientistsolutions.com/index.php?a=protocol