iOS 6 is released today and iPhone 5s will be available on Friday. While a software update or a hardware change on an iOS device isn't nearly as complicated as a computer, there still is some pre-planning involved. Mainly, backing up your data and making sure you're ready for the change. I recommend that everyone take advantage of iCloud backup. With 5GB of free storage for every iCloud account and the availability for automatic backups in iOS 5, it's a no-brainer. But you want to make sure it's running. By default, an iCloud backup should occur automatically at least once a day long as your device is connected to power and Wi-Fi. However, I noticed my iPad hadn't been backed up recently, so now's a good time to check the status of your backups and if necessary run a manual backup.
In addition to iCloud backups, before a major OS update or a hardware change, this is also a good time to have a local backup of your iOS device on your computer. By default when you enable iCloud backups your device stops backing up to your computer. You can run a one-time backup by right-clicking on the device in iTunes and selecting Backup. I do this before any major upgrade. I also recommend that you check the box to "encrypt local backups." Not only will this offer some additional security, but it will enable you to restore all your passwords to your iOS device and prevent having to re-enter them manually.
When setting up your new device you can set it up fresh and re-install, restore from a local backup or restore from iCloud. There are pros and cons to either approach. Setting up fresh is a good opportunity to "clean out the cruft" but you lose all your settings. Of course, plugging in to a computer and restoring from a physical backup is fastest and will restore your passwords if you have the encrypted backup option selected. iCloud restore is very convenient and works like a charm, I've had to rely on that more than once. If you restore from an iCloud backup, you'll need to make sure you're running at least the same or higher level iOS as the one that created the backup, so you may need to check for iOS updates first.
Lastly, you want to be aware of any special apps or circumstances that may not survive a restore of your phone. For example, I use Google two-step verification with my Google accounts and use the Google Authenticator App to manage login codes for my Google accounts as well as other services like Dropbox. If you reset or wiped your phone (or moved to to new hardware) Google Authenticator App might not be able to generate valid codes. If this is the case, you'll have to delete the account, and turn off two-step verification and restart. Better practice seems to be to temporarily disable two-step verification before a planned iPhone restore or upgrading hardware. Google has a help article with more information.