It depends a lot on the market. If it's likely to be used by a lot of medium to large organisations that are unlikely to pirate it (no matter how easy that might be), then you could sell it via a website, with a download, and charge a per-seat license. You'd probably want a 30 day trial type deal, but I wouldn't bother putting too much effort into making it uncrackable. You probably won't have to worry too much about advertising, so long as you come up in the relevant search listings - companies interested in adressing the particular problem you're solving are likely to put in the effort to research options.

Otherwise, unless you have an app that has a really wide appeal (in which case, this should all be pretty easy), you're not likely to turn a lot of profit. You might make a bit of cash from the odd sale, but individuals and small companies don't tend to spend a lot on software, and are used to getting lots of stuff for free.

As already mentioned above, the free (as in beer) route becomes an option. You can make money out of consultancy, support and advertising on your site. But possibly more valuable than all that is the prestige. This can work in a few ways, but apart from anything, it'll look really good on your resume. If you release source code and - for Perl - get stuff onto CPAN, that'll also get you some standing in the community.

Good luck :)