Well the biggest difference is linux is a true multiuser OS by default, its just like having a mini version of a mainframe computer on your desk, many many people can log in and use it at the same time, windows cannot.The other thing is, because its multiuser it has the built in protection from users messing up the core of the OS cause they are separated because they have to be, regular users cannot make system changes, which makes it far more stable and less prone to crash.Even if a user screws up, most of the time the rest of the system keeps on running without a problem.
Another advantage although windows 2000 and XP solved some of this to a great extent is multitasking, the linux kernel is better at handling multiple jobs and making sure they all run as fast as possible.
As far as applications, they share most fo them as far as what most users run most of the time, they may be called different names but they do the same things.I'd have to definitely give the edge to linux when it comes to both portability and automating tasks, linux really shines at that.When it comes to doing real work on a PC, things like file conversions,video editing,video rendering, any utilitarian task, linux blows windows away.
Linux is also more complete as far as what it can do right out of the box so to speak, slackware for example comes with all the server apps,desktop apps,utilities,development languages and development tools, stock, right from the install, these things are extra in windows OR a separate windows product.
The tradeoff is knowledge, it isnt all point and click, and its takes some knowlegde to get some things to work and get some things done, in that respect windows is generally better for the average user.Just like OS X by apple is the same way, its set up for the average person who doesnt know squat about PC's and more than likely doesnt want to either.
