Open Regedit:
Navigate to: HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Run\
Remove entry for Skype.
I have Skype installed and the key looks like (all one line, no wrapping): "Skype REG_SZ "C:\Program Files (x86)\Skype\Phone\Skype.exe" /minimized /regrun
There may be a similar entry under HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\Run\ but the first one will only affect the user account that is currently logged in. The 2nd path will affect the entire system. There may not be an entry under the 2nd one, but I have seen programs place a startup command in both or one or the other. For the record, Skype does not have the 2nd entry on my system.
Chris