You need a Linux OS to run Linux applications, just as you need Windows OS to
run Windows applications. If you have not installed Linux then you cannot use
the applications.

All Linux distros keep applications in repositories. You can install the
applications from a program specifically made to do this called a package
manager. An example of one is Synaptic, but there are several. The repositories
are maintained by individuals with specific training in package management. This
provides a measure of consistency and security for the user. It also helps guard
against dependency problems which can be a problem if you use applications from
outside the repositories.

Generally speaking Linux does not use duplicates of libraries. It uses the same
ones over and over and it makes sure the libraries are of the same generation.
Otherwise you will have dependency problems which means that you have installed
a program that requires certain libraries, but it cannot use them because they
are of the wrong generation. It cannot be resolved because to go ahead would
break your package manager in such a way that it cannot install anything more
until you resolve the inconsistencies.

This is different from Windows where you can have many versions of the same
libraries in different directories and the central registry decides which dll to
use. In Linux there is no central registry and files are put into directories
based on their logical function.

You can install programs in several ways in Linux. The most common and best
choice is to use a package manager which resolves dependencies issues and tracks
where to files are put for ease of de-installation. A second way is to compile
the program from source code which is not for the everyday user as it can be a
lengthy process and takes more advanced skills. The third way is to use
pre-compiled programs which can be made to work with your particular distro.
Some will work out of the box and others require modification using a program
such as alien.

Windows has a few types of executable files, but Linux has many types of
executables (or none depending on how you look at it) and none has a suffix such
as .exe. Files are generally shipped in compressed format such as tar or in
pre-compiled packages which typically end in .deb or .rpm. Some Linux distros
such as Fedora use rpm packages and others such as Ubuntu use debs. You cannot
use a deb on an rpm based distro without converting it to deb format and vice
versa. To complicate matters, one distro that uses debs or rpms may not be
compatible with another that uses the same format. To make this more complicated
still, Ubuntu 7.10 may not run a deb made for Ubuntu 8.04 and vice versa. They
are from different generations.

So having a disk of applications in Linux is rather useless, unless you know
what they are and what distro they are made to run on. I have boxes of CDs with
Linux on them and they are only good for a trip down memory lane. The only thing
that matters with Linux is having access to the repositories and having
applications that were made for my version of Linux.

Unlike Windows Linux ships with lots of applications and every program is free
for the taking. Nobody cares about copying them or distributing them. By
choosing to use Linux you have access to every program made for your distro
without paying a dime. The only advantage to having them on disk is that you
would not have to download them. However, if you have a broadband connection
then you have access to everything and don't have to worry about stroing them or
wondering which disk they are on. You just choose the program from a menu and in
minutes even the biggest programs are installed and ready for use. Oh yes, and
you never have to to re-boot when a program is installed or updated.