HI,
No problem using Skype here Safari 4.0.4 on 10.6.2 so try trouble shooting...
Go to ~/Llibrary/Safari and move the Downloads.plist file to the Trash and relaunch Safari. See if you can download Skype.
If not ...
From the Safari Menu Bar, click Safari / Empty Cache. When you are done with that...
From the Safari Menu Bar, click Safari / Reset Safari. Select the top 5 buttons and click Reset.
Go here for trouble shooting 3rd party plugins or input managers which might be causing the problem.
http://support.apple.com/kb/TS1594
Make sure your MacBook has sufficient disk space. Right or control click the MacintoshHD icon. Click Get Info. In the Get Info window you will see Capacity and Available. *Make sure you always have a minimum of 10% to 15% free disk space at all times.*
Carolyn 🙂