Adobe Reader has a "search multiple files" option, but for that to work, the files need to be in PDF form already, on disk. Ditto for the iFilter, with the files in a location that gets indexed e.g. under "(My) Documents". I don't know much about SqurrelMail itself, so let me have a look ...
Can I assume you're a SquirrelMail
user, not an Administrator running a SquirrelMail server? If so, the
manual makes it appear very simple when it comes to attachment handling, with no "download all" options. Your best bet might be to access the mail through another mail program, such as Outlook or Eudora, thus bypassing SquirrelMail. Your ISP must have details on how to set that up - the makers of SquirrelMail have no way of knowing those settings.