• Do use CGI, or CGI::Simple.
• Do use strict and warnings and CGI::Carp from the start.
• Do use templates (HTML::Template or Template::Toolkit)
• Do write yourself a requirements list if possible.
• Do design the whole thing before you start
  • what administration pages will you need?
  • what sequence of events will customers follow?
• Do create your test cases and scaffolding before you start.
• Do make paper webpage mockups and walk through the client process with a non-geek, perhaps your father?
• Do try to identify all the code you can dump into separate libraries
• Do consider OO where it might be useful.
• Do search CPAN, freshmeat and sourceforge to see if your system or parts of it have already been done before.
• Do ask here to see if we know where it's been done before.
• Do use CPAN modules to do the parts of your project that they can.
• Do make sure that the modules you choose to use are well supported and suit the task you're using them for.
• Do use taint checking. Lots. Always.
• Do expect to throw parts away once you've found a better solution
• Do throw away parts when you've found a better solution
• Do use DBI and its friends if it's DB related
• Do investigate the pros and cons of different databases before starting
• Do read about useability and try to design your system to be useable by a large range of skill levels and disabilities.
• Do think about open-sourcing the end result if you're happy with it.
• Do comment it thoroughly
• Do be consistent in your coding style - and please use one that is considered "standard" (K&R, GNU or another)
• Do try to keep each subroutine less than two screenfuls (ie less than 50 lines) because even if you don't succeed it's a good metric.
• Do try to refactor as much as possible, whenever possible so that your library code grows faster than your scripts do.
• Do test and test and test again. And get someone else to test too.
• Do use a decent change management system such as CVS. Use it properly and tag releases (where it compiles, works and is stable (though not necessarily complete)).
• Do document your module/function interfaces and keep these documents up to date.

Don'ts

• Don't expect it to be easy
• Don't skim on requirements or design
• Don't reinvent the wheel just for the hell of it
• Don't refuse constructive criticism
• Don't write ugly code and then beg us to fix it for you :)
• Don't give up, large projects are a great way to improve at your chosen language.
• Don't use global variables unless you absolutely need to, in fact, don't use them then either.
• Don't hardcode in URLs, filenames, HTML headers, magic numbers. Try to move these to a good localisation module.
• Don't turn strict off. If you need to turn it off, you're probably trying to do something a wrong way.
• Don't keep code just because it took you ages to write it. When you've found a much more elegant/efficient/effective solution, fix your code.
• Don't spend all your time worrying about finding the absolute best way to do something. Do it any way the first time and come back and rewrite at your leisure.

Update:A few more don'ts.