I used to hate .rar files just because WinRAR got really annoying after the trial period.
Then I found The Extractor hxxtp://download.cnet.com/The-Extractor/3000-2250_4-10624213.html?tag=mncol;4
It makes rar files easy do handle, it's free and extremely fast.
And yes, for big collections .rar files are the way to go. For viewing pdf files are great and compatible with practically every device.