Your code contains lot of bad practices:

• &function(...). Correct in Perl 4, still working but with really unwanted side effects in Perl 5. Get rid of all ampersands in front of function names, except when you want to make a reference to a function.
• Two-argument open. Use three-argument open.
• Lack of error checks, especially after open. Unless you use autodie, add or die "Could not open $filename: $!" after open.
• Single-argument system() with hand-crafted quoting. Always begs for trouble, because shells tend to have very different quoting rules. At least pass arguments for the invoked program as a list of arguments. See also Re^3: Perl Rename for a little background, http://www.in-ulm.de/~mascheck/various/ for more.

Also, you seem to go through great pains to handle URLs and to issue HTTP and FTP requests using wget. Perl has LWP, so you do not have to mess with the shell and external programs at all. Look first at LWP::Simple, that should nearly be sufficient to replace wget. If you need more control, look at LWP::UserAgent. As you seem to write a spider, also have a look at LWP::RobotUA.

Perl also can decompress gzip files and unpack tar files, if you like, even both in one package, Archive::Tar, and of course without having to mess with the shell.

For URL handling, look at URI and its helpers.

And for my personal taste, the getFile() function is about 200 lines longer than it should be. Too much code for one function, too deeply nested, too many variables. As a rule of thumb, a function should not exceed one screen, because otherwise, you will get lost in the code. At my university, a screen was defined as a VT420, i.e. 25 lines of no more than 80 characters, but in the real world, my editor shows about 40 lines of about 110 characters. Consider splitting the function into smaller parts.

Alexander