Duplicate calendar, contacts, etc! How to merge?

Ever since iCloud was introduced my calendars and contacts duplicated themselves to have two of each entry on my computer and my iPhone 3GS.

It's super annoying and so un-Apple like!

And now I have an iPhone 5C and can finally start using iCloud, but I still can't get rid of the duplicates, and worse, now all my notes are duplicated too!

How the heck do I fix this?

Why did it happen in the first place? Come on, Apple! Where is the "it just works"?