I presently have a dual-boot configuration on two internal hard drives:
Master: Western Digital 6.4GB drive
Slave: Western Digital 20GB drive

Windows gets the 6.4GB drive; Linux gets the 20GB.

My 6.4gb drive is making noise (it's 5 years old) and I'm going to have to yank it. A new Western Digital 40GB Protege is on its way to my house as I write this. I need to keep Windows for my After Effects work, which is infrequent but still an occasional part of my job duties. But, I am greedy on behalf my favorite OS. When the new drive gets here, I want to set things up afresh and give M$ 6GB of the old 20GB drive, give Linux the remainder of the space on that drive and *all* of the new 40GB drive.

My questions:
1. I know I should archive /home and /etc before I do this. But, will backing up /usr/local allow me to easily restore all the apps that I have installed over the past year (some from RPM, others from source...)? That is important to me.
2. Any matter if I install Windows first, then Linux? Or the other way around?

Thank you for your advice!

1: Should be fine, as long as the app developers installed everything where they should (ie: /usr/local/bin, /usr/local/man,/usr/local/lib) You may find that a few apps break, but most should be fine.

2. Always install Win first, as it will overwrite your boot sector (and lilo or grub) if you install it second