How are the file metadata stored in Windows?

You've been taught that hard disks contain files, but that's not the entire truth. Actually, hard drives contain one very, very big number expressed by a lot of single bits. But this interpretation doesn't make any sense to you nor your computer, because processing single big numbers isn't very common (and I'm talking about REALLY HUGE numbers). Instead, computer splits it into smaller 'words' (8-bit, 16-bit, 32-bit or whatever) and uses like that. Still, that's just a bunch of words (let's assume 8-bit words, i.e. bytes).

Now, that drive is partitioned. I have explained why partitioning is a good idea in this answer:

Generally speaking, drives can be used without partitioning. Most pendrives work like that. But using partitions has many advantages, just to name some of them:

• You can have two OSes sitting on the same hard drive and not interfering with each other. Each one will treat its partition as a logical drive and won't mess with other ones unless you tell it to.
• You can logically separate your data. If one partition becomes corrupted for some reason, other partitions will very likely remain intact.
• Using partitions is better than using multiple smaller hard drives, because your system is quieter, consumes less energy and you can resize, delete, move them around etc.
• You can use some parts of the hard drive for some special purposes.

Now, every partition has its own filesystem. Modern versions of Windows use NTFS, but FAT, FAT32 and exFAT are supported for external media or legacy partitions. Everyday-use Linux installations usually use ext filesystems, ext4 being the latest one.

Filesystem defines the way files are physically located on the disk. You can think of it like this: if you had a 10000-page book without any chapters, page numbers or line breaks, it would be very hard to use. Of course page numbers and chapter titles take up some space on the page, but they make using the book a lot easier and faster. If you want to jump to chapter, let's say, 42, you just look it up in the table of contents. Then you leaf through the book until you find the chapter you want. Your files are chapters and your filesystem is the book. Filesystem metadata, like file boundaries, filenames etc. takes up space too, but it's a comparably small amount of space, and it makes things work a lot faster.

If your "chapter" is empty, it can still have a heading or a page number, right? Empty file contains zero bytes of data. Metadata takes up space, but it's not a part of the file, but of the filesystem. Otherwise you'd see filenames inside your text files?

By the way, that's why early versions of DOS were accepting only 8.3 names - the space reserved for filenames was very limited. NTFS allows filenames that are 255 characters long^[1].

Just one more word on your comment:

I used to have a kind of virus that somehow corrupted a couple of files in my PC so that they appeared to be about 100GB in size. Each of them. On my 40GB harddisc. So there must've been some kind of magic... :-D

That's completely possible to have valid files bigger than your hard drive thanks to a feature called sparse files. Hennes has an excellent explaination of these in his comment on this question:

Imagine a binder capable of holding a 100 pages. If you use that binder as a regular file you could insert a 100 pages. You could read all 100. You could write to all 100. Now imagine a sparse binder. You insert the first page you write "page 1: Content A". You then insert a the second page you write "page 9999: content b:". Whenever you try to read a page you look if it exists. If it does not, your answer will be this is an empty page. If it does exist you return the contents of the page. Whenever you write to a page which does not yet exist in the binder you add a new sheet of paper.

Just learned today about Windows Alternate Data Streams (ADS). This is a hidden resource fork that is attached to a file. It has been part of NTFS since Windows NT 3.1.

For example, if you have a blank text file but fill in some of the summary information in the file's property tag, a hidden ADS file is created and attached to the text file. Most versions of Windows don't include the size of the ADS file when reporting the size of the original file.

You can create and view ADS files from a command prompt.

echo "ABCDE" > test.txt:hidden.txt

will create a test.txt file with an ADS file called hidden.txt

you can use this command to edit the file:

notepad test.txt:hidden.txt

Here's an easy to read article that goes into greater detail.