If you have different accounts it would be easiest to sync with different iTunes libraries. Create a new user for your wife on the computer, then log into that before connecting and syncing the iPod Touch. When you first connect it, it will probably warn you about erasing content. If you see a Transfer Purchases option do that. If not cancel the dialog and manually select the Transfer Purchase option by right clicking on the iPod Touch in the left column and choosing Transfer Purchases.
If you decide to continue using the same library, just go through all the sync settings when the device is attached (tabs at the top of the page). There may be some leakage due to other settings, but for the most part iTunes will remember what is supposed to sync to each device. You'll also need to be aware that any apps you end up sharing across devices can only be updated using the Apple ID they were purchased with. That will mean signing into and out of each other's accounts in the store apps on the devices. If you are not going to share any apps or content, the separate library strategy is still your best/cleanest way of doing things.
If you do end up using each others accounts and apps on the devices you'll also want to go into the Store settings on each device, and Preferences Store on the computer. Turn off the automatic Books, Apps, and Music syncing. Unless you want new content to automatically go to the other devices (when they are signed onto the same account).
