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Chunked uploads is intended to provide better reliability during the upload of large files using the Upload Wizard. In addition, it allows a greater maximum file size (500mb as opposed to the usual 100mb). However, chunked uploads is still experimental and uploads may give unexpected errors.
Chunked uploads are not supported by all browsers. (They require slice-method which was introduced in Firefox 5, Chrome 6). During a chunked upload, the file is split into 5 MB-parts and these parts are uploaded. If some parts failed to upload, the whole file does not have to be re-uploaded, only the parts that failed. All this is done in the background in UploadWizard.
It provides better reliability not just for UploadWizard, but also for bots using the API, especially for files uploaded through the API.
At this point in time, Chunked Upload support is in experimental testing. You can activate it in your preferences, in the “Upload Wizard” section under “Experimental features”, and help with further testing. Please report test results on the talk page (you can also note broken files which need to be removed).