Starting from the release of Skype 2.7 for Mac, your general system startup settings will be used instead of having separate preferences for Skype.
To prevent Skype from opening on Mac OS X startup, open Skype and go to the Dock. Use Ctrl+click on the Skype icon in the Dock and ensure the box "Open at Login" is unchecked.
Alternatively, you can go to System Preferences > Users & Groups, click your account name and select Login Items. Remove Skype from this list.