most linux distros now come with helper progs that will convert a dos command to it's corresponding linux equivalent - but it's a really bad idea to rely on that. every dos command has a linux command that does everything it does, and probably much much more. shell scripting in any *nix is much more advanced than msdos scripting.
as far as encrypting files, you'll need to get a package or a program for that. you can always find stuff like that on freshmeat.net or sourceforge.net.