I'm starting out with force.com development, and I'm currently a little hazy about what the above terms all mean. Could someone give an overview, and if possible explain how permissions are defined on each one (if at all)?
To put it all together, you could say something like:
John Doe is a salesperson for ABC, Inc, and is a user in their organization. He is the owner of the Acme account. He has the Salesperson role, which is subordinate to the Sales Manager role, so his manager can see all his records. He has the Standard User profile, so he cannot perform administrative functions in Salesforce.
I'd also recommend that you take a look at the API doc, which explains all the entities and has relationship diagrams.