Transforming your development environment by following all the principles described here is not an easy task, but the benefits are enormous:
A modular architecture enables you to efficiently divide tasks among multi-disciplinary teams, cutting overall development time.
The use of all the features of the object-oriented paradigm makes your code more readable and reusable, decreasing the development effort in subsequent projects.
PEAR and its package system help you keep track of dependencies among different modules of your code base.
Using the Template View Pattern will make layout integration avery pleasant task.
Finally, the handler.php approach will keep you focused on what really matters, leaving all the layout details out of the development cycle.
We also recommend that you pay close attention to these topics:
Choose the right version control software to fit your needs, and make sure your team is using it in its daily work.
Always use unit testing if the volume of the code you produce starts to grow. If you don't, you'll easily lose track of all the modules you developed and what tests you should run to make sure they're safe for production.
Profiling and benchmarking
How can you improve the performance of your application if you don't really know where it's lagging? Get a decent profiling tool and analyze your code thoroughly before every deployment.
Always document your own code and follow some documentation standard within your team. Make documentation widely available to every team member.
So, what are you waiting for? Go ahead and start implementing these methodologies, and always keep track of your changes so that you can measure your improvements.