[eluser]IgnitedCoder[/eluser]
As common practice for me I generally drag the application folder out of the system folder so I can update CI easily... so instead of:
system
index.php
I cut the app folder and then I have. so if a new CI version shows up its easy to replace the system folder. Its just cleaner I guess/think.
application
system
index.php
I generally template out my header, footer and content
so view generally have a template folder
view
templates
Then I seperate out each view by controller
views
home
login
browse
etc.
I realize you didn't ask for this much detail but I figured it couldn't hurt to share.
Brendan