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The Full screen mode is able to change the resolution, colour mode and refresh rate of the screen, while windowed runs using the current desktop settings. It can take monitors a few seconds to adjust to new screen modes, which is why they tend to go black for a bit when you start or alt-tab a full screen app. Windowed mode apps don't have that delay.

A full screen mode app will lose it's device when it loses focus. If you have a dual monitor setup and you click the mouse on the monitor other than where a full screen app is running, the app will disappear until it has focus again. This got REALLY annoying for me in WOW years ago, until I discovered the setting for borderless maximised windowed mode (looks like full screen, but has the app/focus switching speed of windowed).

There's more full screen details in the directx sdk help files, going into stuff about swap chains, exclusive mode access, multihead issues, etc.
^{(Posted by Kojack in this forum topic.)}

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In full screen mode the application is not windowed.

That's essentially what it is.
No cooperation, no syncing, no nothing.
Which is why it's usually faster.
^{(Posted by jacmoe in this forum topic.)}

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For debugging it's better to disable the full screen mode.