The advantage of shell scripting is that it's globally present on *ix boxes, and has a relatively stable core set of features you can rely on to run everywhere. With Perl and Python you have to worry about whether they're available and if so what version, as there have been significant syntactical incompatibilities throughout their lifespans. (Especially if you include Python 3 and Perl 6.)
The disadvantage of shell scripting is everything else. Shell scripting languages are typically lacking in expressiveness, functionality and performance. And hacking command lines together from strings in a language without strong string processing features and libraries, to ensure the escaping is correct, invites security problems. Unless there's a compelling compatibility reason you need to go with shell, I would personally plump for a scripting language every time.
