Linux doesn't use file extensions, it's clever enough to tell a file's type by the magic number (the first couple hex codes) at the start of the file.
Gnome and KDE are Desktop Environments, in the same way that Explorer is the Windows DE. There are too numerous differences to list them here. They are different means of achieving the same end - a intuitive user interface for X11. There are other window managers besides those two though. I personally prefer fluxbox.
The X windows System is the means for displaying a windowing environment on Unix-like machines. Unlike MS Windows it does not provide any means of manipulating windows graphically (i.e. no frames, borders, dragbars, etc) it leaves that up to a Window Manager which sits on top of X and makes requests to X to resize etc based on what the user clicks. This seems complex (and it is) but it provides an extremely flexible sollution to windowing that allows the user to use any number of Window Managers or even create their own.
Applications can run on multiple distros if they are statically linked to any libraries they use. Most commercial applications will be done this way. The only reason packages are for specific distros is because they will link against the specific version of a library in that distro. This is why when you compile stuff it doesn't matter what distro you use because it will just link against which ever library versions you have installed.
The compilation routine has to be flexible because source code has to compile against several types of C compilers and various library versions. Linux users generally use GNU compilers, but it's possible to use others and users of BSD / AIX / SJD / HP-UX etc won't necessarily be using GNU compilers. Don't forget source code has to compile for them too. The ./configure / make / make install path is flexible enough to allow compilation on different architectures.
BeOS is only similar to Linux in the sense that they are both POSIX compliant. Linux binaries won't run on BeOS and vice versa. BeOS uses a BeOS kernel, Linux uses the linux kernel
There are several distros designed to look like windows, but in honesty if you want windows then use windows
There are a few proof-of-concept linux viruses, but nothing with any real threat. The difference is that in windows any user can alter the system. In linux only the super user can. Therefore for a virus to be effective it has to be run as super user. If you're sensible and only log in as a normal user then the chances of something terrible happening are remote. A lot of windows viruses work on the assumption that users use a particular program for a task - e.g. a virus might exploit a bug in Outlook Express knowing that 90% of users use it. In linux there is so much choice that there's no guarantee people all use the same programs for a task. Also, the open source nature of most programs means that any potential security holes are likely to be spotted by someone, somewhere, analysing the code. The short answer is that the threat from linux viruses is virtually nil.
Start-Up and Start-Menu would be different depending on the window manager you use. Likewise desktop.
System wide config files are under /etc somewhere. Config files specific to a user are dot files (hidden files start with a . ) in the user's home directory. E.g. my vim config file is .vimrc in my home dir.
ps ax
pstree
both tell you running processes. The "nice" command will let you assign priority to a process. Type "man nice" to read the manual page. That goes for any other command too...(eg: man man)
Yes, your choices for a dual system network are either running Samba under linux (the easier choice) or getting your windows machines to play nice with NFS (which is actually a damn site easier to set up on linux, but windows support for it is patchy)
Download something that is autopackaged...such as their null package or GAIM, make the autopackage executable and then run it 
