I think Joomla comes with a media management system (with PDF support as well), which allows you to upload/browse files, I'm not sure how flexible it is but it should be skinnable.
Also, look for Document Management Systems (DMS) in Google and you'll find quite a few.
If you have average coding skills I'd suggest taking ScriptMan's advice, go commando, code it yourself 
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Hades,
Ancient god, King of the Nether World, and Guardian of the Dead.
...and on my free time I'm also a web developer, contact me if you need one!
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