Start with Scotland's People: Connecting Generations. You must register to perform searches. Here you can search census, vital and probate records for free; pay per view to see records.

Scotland GenWeb (scroll down to find the links to the county sites.)  

Scottish Genealogy Society
(they publish The Scottish Genealogist as well as maintain a library --in Edinborough, of course-- and sell publications helpful for researching in Scotland.  See also their links to member websites)

GEN-UKI page for Scotland

Dept. of Geography, University of Edinborough has a very helpful page " Tracing your Scottish Ancestry ".

Scottish Archive Network allows you to search the catalogs of dozens of
" Rampant Scotland -- For Everything About Scotland" has a  genealogy page as well as a wealth of other information about the country.

Map: Clans of Scotland

Dictionary of the Scots Language

Cyndi's List: Scotland