Starting from the release of Skype 2.7 for Mac , your general system startup settings will be used instead of Skype having it's own preferences.

In order to prevent Skype opening on Mac OS X startup, open Skype and go to the Dock. Use ctrl+click on the Skype icon on the Dock and ensure the box "Open at login" is unchecked.

Alternatively you can go to System Preferences > Accounts, click on your account name and select Login Items. Remove Skype from this list.