The plugin can also be called on an element containing the file upload form.
If you define the url, method and fieldName Options, you can call the plugin on any element - no form or file input field required - and the drag and drop functionality will still work. The file input button functionality will also work without a surrounding form.
But without support for iframe uploads, you will leave users of IE and Opera out in the dark.

Using the dropZone option, you can define a container inside of the form or anywhere else on the page as dropZone target. You can also adjust the CSS code so the file input field does not cover the whole form.

Please have a look at How to submit additional Form Data, specifically the second section about "Sending additional Form Data by adding input fields to the upload form".

The file upload plugin makes use of iframes for browsers like Microsoft Internet Explorer and Opera, which do not yet support XMLHTTPRequest uploads. They will only register a load event if the Content-type of the response is set to text/plain or text/html, not if it is set to application/json. Setting the content-type of the JSON response to "text/html" should usually fix problems where IE shows an unwanted download dialog.
Please have a look at the Setup instructions.

Your JSON response is probably not valid JSON.
You can test your JSON response for validity on jslint.com.

You can use the accept attribute of the file input field to limit the file type selection, though this seems to be supported only on Google Chrome and Opera.
An example limiting files to PNG images:

<input type="file" name="file" accept="image/png" multiple>

Note that this will not limit files added by drag&drop and is not supported across all browsers.

It is possible to upload large files (> 1 GB) with the jQuery File Upload plugin, but with some reservations.

HTTP might not be the ideal protocol for uploading large files. Until the Blob API get's better support across browsers and allows chunked file uploads, there is also no support to resume aborted uploads.

Apart from the implementation used for Firefox 3.6 (and other browsers which support the File API and XHR file uploads, but not the FormData API), the jQuery File Upload plugin doesn't put anything on top of the HTTP upload implementation of the browser. So any files that can be uploaded with a simple HTML form upload can be uploaded with the jQuery File Upload plugin as well.

See also issue #103.

Invoking the click event on a file input field is not supported on the following browsers:

• Firefox 3.6 (tested on OSX and Windows XP)
• Opera 11.01 (tested on OSX)

It works on the other major browsers including Firefox 4, so it might be a feasible solution in the future.

See also issue #92.

The plugin is meant to be used by developers who can easily customize it and adapt it to work with their server-side web application framework.
However, since version 4.0 an advanced PHP based example has been added. If you need more inspiration you can have a look at the Demo implementation or the various user-contributed tutorials on different server-side implementations linked on the Wiki homepage.