I’m not a very competent perl programmer. Even writing the word programmer here makes me slightly embarrassed. I do carry out frequent sequence conversions and manipulations with perl scripts I’ve put together though. Sometimes when I need to run a script many times I’ve found the most irritating thing is launching the scripts and pointing it towards the right input file. A much simpler option in this case is to save the script as an application and drop the files onto it to carry out the conversion. I’ve come across two options for doing this (all this is very Mac-centric I’m afraid but I’d be interested to see MS equivalents in the comments).
The first is the open-source program Platypus by Sveinbjorn Thordarson that “can be used to create native, flawlessly integrated Mac OS X applications from interpreted scripts such as shell scripts or Perl and Python programs”. Make sure that the “is droppable” check box is selected. I found it quite straightforward to turn scripts into droppable applications this way. As it says on the site, but it needs some remembering, you will need to modify your script slightly to accept the infile correctly. The basic tutorial page says the following

Enabling “Is droppable” for an app will modify the property list for for the app in question so that it can receive dropped files in the Dock and Finder. These files are then passed on to the script as arguments via @ARGV. However, the first argument to the script ($ARGV[1], $1 etc., depending on your scripting language of choice) is always the path to the application bundle (for example “/Applications/MyPlatypusApp.app”).

Essentially this means that (in perl at least) where your input file would be identified right at the start by @ARGV[0] it should be changed to @ARGV[1] before creating your application.
Another interesting aspect is the ability to bundle in code files referred to in your script. This means for example that if you have a script that depends on bioperl, it needn’t break, just add in the path to the parts of bioperl needed.

The second option is an AppleScript droppable application. I have to admit that I have never written an AppleScript but I came across this post recently from TUAW outlining the “do script” command. Applescripts can be saved as dropplet applications onto which you drop input files. A bit of Googling reveals people using both do script “script.pl“ and do shell script “script.pl”. The last seems a bit odd since script.pl is a perl not shell script, but it looks like either will work.
As an example I once created a perl script that took an alignment in a range of formats and converted to a format acceptable to phyml, then ran the program using standard settings of my choice. I have this on my desktop as a droppable application called “runPhyml”. It works very nicely for generating quick trees.