Each iPhone will have a separate backup with iTunes on the same PC especially if each iPhone has a different name.
iTunes content can be transferred to an iPhone from a single computer only. When syncing iTunes content with a another computer, all iTunes content that was transferred from a different computer will be erased first. The same applies to photos transferred to an iPhone via the iTunes sync process.
This does not affect any other data on the iPhone.
Each iPhone can have its own sync preferences with iTunes on the same PC. Best to disable automatic syncing. iTunes includes a global setting for this at iTunes > Preferences. Under the Devices tab select disable automatic syncing when an iPhone or iPod is connected.
When she connects her iPhone to iTunes on your computer, do not sync. Control-click on the name of the iPhone in the iTunes source list and at the pop-up menu window that appears, select Back Up. This will create a backup for your wife's iPhone that will be separate from your iPhone's backup.
This link provides the data that is included with the iPhone's backup.
http://support.apple.com/kb/HT1766
If selected, deselect syncing any iTunes content under the Music, Video, and Podcasts tabs, and the same under the Photos tab - unless she wants to transfer selected iTunes content and any photos from your PC to her iPhone.
When she connects her new iPhone to iTunes on your PC, she will be prompted to transfer one of the available iPhone backups. She can select the backup created for her existing iPhone via the pop-up. This will transfer all the data included with the iPhone's backup. She can follow this by syncing iTunes content and and photos from your PC. If you don't want your contact info co-mingled, do not select sync contacts with a supported application on your computer under the Info tab for her iPhone sync preferences.