If you want to use tags, then you might look at Things.
For OmniFocus, I would suggest you read David Allen's "Getting Things Done". OmniFocus is based on that productivity methodology. I think you won't fully understand the power of OmniFocus if you don't understand and follow GTD.
Folders are just a way to organize groups of things. So for instance, you might have a folder labeled Personal and another labeled Work.
Projects would generally reside inside a folder (though they don't have to). They are the meat & potatoes of GTD. A project is any task that has more than one related physical action. So for instance, a project might be "Clean Out The Garage". Then inside that project would be a number of actions like "throw away trash", "buy shelving", etc.
Additionally, a project can be structured to be sequential or parallel. Sequential means you have to do the actions in a certain order. Parellel means that you can do the actions in any order.
Actions are any single physical action. Don't be tempted to make an action called something like "Clean Out Garage", because that isn't a SINGLE physical action - it is really several actions. Therefore, it would be a project.
A Single Action List is just a way to group actions that are unrelated. You could use a folder for this if you want, but a Single Action List has a little more power because you can assign a start date, due date as well as other features.
And I didn't even begin to explain contexts or whether or not to use due dates... that's a whole 'nother discussion.
Hopefully that isn't too confusing. Again, I would highly recommend you read David Allen's book. He goes into much greater depth about all of this stuff.