Linux uses a different approach to file systems. There are several different
formats for Linux. Ext2 and ext3 are most common. There is an ext4 in
development. There is also ReiserFS which is what I use with Reiser4 in
development. I am no expert, but this is my understanding.

Basically Windows files systems start at the beginning of the drive and add
files continuously from there. As files are added the old files have no room to
grow so they add fragments in other locations using the first available
location. One file can therefore become spread in several different locations
which causes the system to slow down over time as the drive continually is
seeking various parts of the file. Defragmenting is needed to pull all of the
parts together into one contiguous block. Of course the process of fragmentation
begins all over once again.

Linux file systems do not place new files right next to previous ones. It
spreads them out, allowing each file room to grow. As files grow closer together
they can be moved into larger available blocks. Linux manages this in the
background for the most part. Drives can become fragmented as the drive
approaches 80% its capacity as there is little physical space to put large
files. As mentioned by someone else it does periodic checks at boot up to
maintain overall integrity. Linux uses a journalled file system (Reiser, ext3,
but not ext2). This means that changes to files are logged so that if the power
goes out the file system is less likely to become corrupted.

Linux does not need to worry about the registry either because it does not have
one. Instead files are stored in a hierarchical file system where the
directories have significance and the individual programs have their own
configuration files. Linux knows where to look because of what directory the
files are stored in. If a config file is corrupted, and it can happen, it does
not affect other programs or the OS in the same way that a corrupted central
registry can.

Linux is different. Notice that I did not say better. You can mess up any file
system no matter how good if you are not careful. And with diligence Windows
file systems and registry can be kept in good shape. The problem is that many
novice Windows users do not exercise diligence.

Windows has had to make compromises in order to keep backward compatibility with
previous versions. Their FAT file system is very old, some would say venerable
as it is still in use. NTFS suffers from fragmentation as any XP user can
attest. Vista was supposed to have a new FS called WinFS, but it was one of the
things they cut. Again it is hard for MS to make a break because Windows users
want backward compatibility. The next Windows OS called Windows 7 should be
different. I hear on the blogosphere (or rumor mill) that it is being fast
tracked due to problems with Vista. It is said to be modular and people are
likening it to what Apple did when they moved to a BSD based OS. We shall see.
As we learned from Vista, MS will cut things at the last minute, especially if
they are pushing up the release date.

Here is an interesting blog from a KDE developer griping about the kernel and
how it slows KDE down: http://www.kdedevelopers.org/node/2270

It is all a matter of perspective. If we think that Linux is perfect then it
can't get better. There are always things to improve upon.

Here is a fairly untechnical description of the ext file system:
www.nondot.org/sabre/os/files/FileSystems/ext2fs/