An iCloud account, iTunes account and Apple ID are all the same thing. Apple just refers to them a bit inconsistently. You can (and typically should) have a single Apple ID for all of them, unless you specifically need to separate them out.
Typically refers to the Apple ID that is used for iCloud services, such as backup and syncing documents and settings between apps. This is set in Settings → iCloud → Account.
The Apple ID that you use to purchase downloads from the iTunes, iBooks and App Stores and what syncs your iTunes Match songs, if you use that service. It's set in Settings → iTunes & App Stores → Apple ID.
It's important to note that your purchases are linked to your Apple ID (although music is now DRM-free), and are not transferrable to other Apple IDs. So you should be sure to make all your app, video and music purchases on a single Apple ID to save yourself future headaches.
Your Apple ID is also used for iMessage. Set in Settings → Messages → Send & Receive.
Using Multiple Accounts
You can be signed in to different accounts for each of these services, which can be useful if, for example, you want to have a single family account for iTunes purchases, but keep your iCloud and iMessages separate.
Apple has a few support pages that are helpful for untangling all the intricacies of the Apple ID: