I use Skype on linux and the client is quite limited in terms of buttons etc, which doesn't bother me at all since I don't use a mouse unless I must (answering skype calls forms a lot of the "must"!). In group chats however, its annoying to have the alerts popping up all the time and I don't have a menu option to stop them. To disable them I discovered I can just use:

/alertsoff

The / lets skype know its a command - much like IRC! There's a full list I found on Skype's support site, very handy :)