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It is pretty much like AdultKing said.
If the domain is registered through GoDaddy and you already have a godaddy account - the owner will simply initiate a free account-to-account transfer. You will get an email from godaddy with instructions on how to login to your account and accept the transfer so the domain shows up in your account and gives you full ownership.
If the domain is registered at GoDaddy, but you do not have a godaddy account and prefer to transfer it to your favorite registrar, say NameCheap..then you can visit namecheap and initiate a transfer. The owner of the domain will need to provide you with an EPP Code which is used to initiate the transfer out of godaddy and over to namecheap.
That is about it as far domains are concerned. As for the website, adultking also pretty much summed it up. The owner of the website will usually just export the database and zip the files and send them over to you. If they do that you just create a database and database user, add the user to the database, login to PHPmyadmin and use the import feature to import the database file. Then, just unzip the files and upload them to your hosting account - don't forget to update the nameservers on the domain..and you're done.
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