I attended a talk at YAPC::NA 2012 where genehack went through some of his tools. I cannot find a copy of the talk anywhere (anyone?) (thanks forzenwithjoy - http://www.youtube.com/watch?v=REeM8h1e9bI), but he had some pretty good suggestions. A few that came through the fog / hit close to home:

• Set your editor to save with the correct whitespace settings. How many times have you done a commit 'did x', immediately followed by a 'whitespace fix'?
• flymake making use of perl -c
• fylmake making use of perltidy (could also apply to htmltidy, jslint, and so on)

I also use a few more (but my configuration is not yet on github):

• org-mode - general note taking, hours tracking, outlining, charting, and so on.
• unittest.el - Turns an indicator on the status bar green, red, or orange based on return value. I may replace this with a flymake-based solution at some point.
• ecb - Emacs Code Browser. A nice module to manage the screen layout when working with code.
• perl-mode or cperl-mode - preference of the user. If code is confusing to one, simplify the code or try the other mode.
• flyspell - mark spelling problems as they happen.
• I am also working on something using Devel::Cover based on rcov-overlay. I may veer off on a new implementation strategy for this based on fly-make (thanks for the inspiration genehack).

Update: Changed link for genehack's github account to his full directory. The original emacs repository is an ELPA load script.