僕のflymake-perl周りの設定晒し最終版（今現在）

(require 'flymake)
(require 'set-perl5lib)

(defadvice flymake-report-status (before flymake-quite-report-status (e-w &optional status))
  (if (not e-w)
      (progn
        (flymake-mode 0)
        (flymake-log 0 "switched OFF Flymake mode due to unknown fatal status (maybe tramp is running)"))))
(ad-activate 'flymake-report-status)

;; エラーをミニバッファに表示
;; http://d.hatena.ne.jp/xcezx/20080314/1205475020
(defun credmp/flymake-display-err-minibuf ()
  "Displays the error/warning for the current line in the minibuffer"
  (interactive)
  (let* ((line-no             (flymake-current-line-no))
         (line-err-info-list  (nth 0 (flymake-find-err-info flymake-err-info line-no)))
         (count               (length line-err-info-list)))
    (while (> count 0)
      (when line-err-info-list
        (let* ((file       (flymake-ler-file (nth (1- count) line-err-info-list)))
               (full-file  (flymake-ler-full-file (nth (1- count) line-err-info-list)))
               (text (flymake-ler-text (nth (1- count) line-err-info-list)))
               (line       (flymake-ler-line (nth (1- count) line-err-info-list))))
          (message "[%s] %s" line text)))
      (setq count (1- count)))))

;; エラー、ウォーニング時のフェイス
;; via http://d.hatena.ne.jp/antipop/20080701/1214838633
(set-face-background 'flymake-errline "red4")
(set-face-foreground 'flymake-errline "black")
(set-face-background 'flymake-warnline "yellow")
(set-face-foreground 'flymake-warnline "black")

;; cperl-mode
;; もし何かあったら http://www.bookshelf.jp/soft/meadow_41.html#SEC608 へ
;; cperl-mode is preferred to perl-mode
;; "Brevity is the soul of wit" <foo at acm.org>
(defalias 'perl-mode 'cperl-mode)

;; Perl用flymake設定
(push '("\\.pl$" flymake-perl-init) flymake-allowed-file-name-masks)
(push '("\\.pm$" flymake-perl-init) flymake-allowed-file-name-masks)
(push '("\\.t$" flymake-perl-init) flymake-allowed-file-name-masks)
(push '("\\(.*\\) at \\([^ \n]+\\) line \\([0-9]+\\)[,.\n]" 2 3 nil 1) flymake-err-line-patterns)
(add-hook 'cperl-mode-hook
 '(lambda ()
    (defadvice flymake-post-syntax-check (before flymake-force-check-was-interrupted)
      (setq flymake-check-was-interrupted t))
    (ad-activate 'flymake-post-syntax-check)
    (define-key cperl-mode-map "\C-cd" 'credmp/flymake-display-err-minibuf)
    (set-perl5lib)
    (flymake-mode)))

（追記）
　うーん、実際にやると、エラーメッセージが表示されてどうなってるか分かりにくい…。(message-box "flymake-mode is off!!")とかはさんでおくと、実際に実行されてる（２回も！？）のが確認できるんですが。