For anything involving mainly the manipulation of files, external commands, or processes, I'd use Bash (or, more correctly, a shell script). For anything involving mainly the manipulation of structured data, I'd use Perl. For anything involving both, I'd use both (to the extent that the problem isn't so simple that you can handle it with sed or awk; and even then, Perl is often a good choice).

Perl has a lot of strengths specifically because it was designed as a glue language to "fill in the gaps" where system calls or data structures were not straightforward to handle with existing tools; arguably, the end result isn't always very elegant, but it often gets the job done where previously you would have had to resort to a small custom C program.