initUpload and beforeSend are called for each selected file.

[MarcDiethelm]

If this is the intended behavior I think that makes those methods pretty useless. In my use case I need to prepare data about ALL the files before uploading the files, and I therefore need to know when the user is ready to upload...

If you agree I will try to make a patch...

[blueimp]

I completely disagree, but I'm the plugin author. ;)

I've updated the Options documentation with a note regarding the callBack being called for each individual file.

By default, the plugin uploads each selected/dropped file individually and asynchronously. Therefore, in my opinion it makes perfectly sense to have a separate callBack for each individual file.
It is also possible to select and drop additional files while there is still an upload under way.

However you also have the option to upload multiple files with one request, which will result in only one call to initUpload and beforeSend.

Also, even with the asynchronous individual uploads, you can delay the uploads with the beforeSend function and do your data preparation before any upload starts.
Have a look at How to queue files and start uploads with a button click.

[MarcDiethelm]

Ok. I see what you mean. Pretty cool...

My use case is as follows:

The user selects a bunch of files. Now he has the option to enter metadata for each file and upload them one by one OR he can just click a button that says Upload All (async is fine).

1. The plugin as it stands can be pre-configured to do one or the other but not both, correct? What's your opinion on that? :)

Also if I add a Upload All button and set a click handler in the beforeSend callback (multiFileRequest=false) I'll end up with as many click handlers on the button as there are selected files. (I can unbind all click handlers before adding a new one, but it feels dirty).
2. So I think it would be nice to have an additional callback that tells me that the user has completed a file selection.

Also your code could use some documentation! I have trouble understanding what happens when and where. I love closures but sometimes it gets pretty confusing. :)

[blueimp]

Have a look at How to queue files and start uploads with a button click and How to submit additional Form Data.
Modifying the buildUploadRow and Using the beforeSend method, you can add fields that add metadata for each individual file upload and still have a button that will start all File uploads at once.
So, the answer to your question N°1 is "No, it can do both".

Have a look at the documentation I linked above, you only need one click handler for an "Upload All" button.

If you still feel the need for a general callBack for "files selected", just do this:

beforeSend: function (event, files, index, xhr, handler, callBack) {
    if (index === files.length -1) {
        // Your code here will only be called once for a file selection (multiple or single)
    }
}

Yes, better documentation is always good. Eventually, I should also add some more comments to the code itself.
But the Wiki is growing and is also a good place for user contributions. ;)