There are a few options.
A - As mentioned above, Google should sync your apps back to your device after the wipe. Everything on your virtual SD card you will be responsible for yourself. Data and settings for most of those apps will be lost as well.
B - Use an app to backup the apps, Astro and My Backup for example I believe can do this. This still doesn't back up your data and settings or stuff on the sdcard.
C - Use the built in backup via command line. I haven't used this method, but it sounds good in theory. Essentially you plug your phone into your PC, type in a line or two, your phone makes a backup and sends it to your PC (I am not sure if it automatically backs up SD card data, so you probably will still be personally accountable for it). But then you would unlock, let it wipe your device, and then root your device. Once rooted (do not install a custom ROM yet), restore your backup. Once your backup is restored, use something like Titanium Backup or My Backup to make a rooted backup if you plan on changing ROMs.