What's your preferred IDE?

Currently, still, it appears to be screen/byobu plus vim.

Probably I am missing all the niceties of something like netbeans, but here's how I set up a cakephp environment:

create a file that contains paths to sections...
---BEGIN FILE ---
cd /path/to/app/Controller
screen -t Controller
cd /path/to/app/Model
screen -t Model
cd /path/to/app/View
screen -t View
cd /path/to/app
screen -t app
cd /path/to/app/webroot/js
screen -t js
cd /path/to/app/webroot/css
screen -t css
cd /path/to/app/webroot/tmp/logs
screen -t logs
---END FILE ---

If you're using tmux instead of screen:
---BEGIN FILE---
cd /path/to/app/Controller
tmux new-window -n Controller
cd /path/to/app/Model
tmux new-window -n Model
cd /path/to/app/View
tmux new-window -n View
cd /path/to/app/
tmux new-window -n approot
cd /path/to/app/webroot/js
tmux new-window -n js
cd /path/to/app/webroot/css
tmux new-window -n css
cd /path/to/app/tmp/logs
tmux new-window -n log

---END FILE---

then simply source the file when you want create the screens for our application
To change between screens, the default mappings of ctrl-a, number will get you there.

I also use :split within vim to work on multiple documents within a given structure. I find this *generally* gives me a quick and easy way to handle the substructures I need and keeps me organized. The few other things most IDEs also have (like class trees and completion) I haven't yet had to use, but I figure I could also macro that as I need. On the logs screen, I can tail -f debug.log.