I like curly-bracket block formatting, myself:

main {
    root=/path/to/root
    filepath=/path/to/files
    ftp_instances=01 02 03
}

ftp01 {
    sourcepath=/source/path/on/server
    savepath=/save/files/here
}
[download]

If you've never used Parse::RecDescent before, the above is a great way to learn. The grammar for the above is fairly simple.

I don't really like the look of XML files, but they do have the advantage that, using XML::Simple, most of the work is already done for you.