What I have done is create an html page with a .swf or .fla file and name it index.html. This will be the first page that loads. You can then link your logo on your splash page to your Joomla! main site.
Better yet, have joomla in a folder (not on webroot), I find it easier to manage especially when I have to use joomla, a bb software, a picture gallery, etc..
Now if you don't want a splash page, a simple php redirect to joomla folder.
Or else, design your splash page and place it at web root.