I find the Command Reference Guides at http://www.cisco.com/en/US/products/ps6441/prod_command_reference_list.html very valuable (especially for study).
However I would propose that instead of having the commands all sorted alphabetically that they be grouped by what they relate to.
For example, every command relating to HSRP (standby commands) be grouped together under a section. The reason for this is because unless you are very experienced (and probably don't need to refer to the reference guides), you have no way of really "knowing" all the options for a specific technology.
I often check the technology areas but when comparing the commands available I often see ones included in the Master References that aren't listed under the specific technology areas (or at least in one complete document) - maybe they are split apart over multiple docs.