This has been covered recently in this forum. Go to the Mac's System Preferences. Open the Accounts preference pane. Select your account, then click on Login Items. Scroll down until you see Skype. Highlight it. Next, click on the 'minus' symbol at the bottom of that window to remove it from your startup items. Next time you fire up the computer, Skype will not auto-start.
reference: http://forum.skype.com/index.php?showtopic=112545&view=findpost&p=509592&s=95b90ee2e5c9cbdf86801ff004fcfcc5
