No. The "file" upload field that browser support normally can only be used to upload a single file. One file goes in one field and is uploaded at once.
You can certainly put more than one field on your form. You can even use JavaScript to add lots of fields automatically as the user uploads more files. But the user will have to browse separately to each file she wants to send you.
Using pure HTML, it is not possible to upload an entire folder with one click.
It is possible with a Flash upload script to let your user pick more than one file at a time and upload them all at once. I haven't personally heard of doing this with a Java applet, but that doesn't mean it isn't possible.