I use emacs with cperl-mode and perltidy. I've added the following to my .emacs file:

(defun perltidy ()
  "Run perltidy on the current region or buffer."
  (interactive)
  (save-excursion
    (unless mark-active (mark-defun))
    (shell-command-on-region (point) (mark) "perltidy --profile=/home/
+foo/.perltidyrc -q" nil t)))

(global-set-key [(f5)] 'perltidy)
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Then I simply mark a region and press F5 to indent it nicely (according to my settings in the /home/foo/.perltidyrc file.