..., we are considering adding a larger hard drive to my wifes laptop, transferring all the data to it and using it as our main computer. ...
From your OLD computer...
Copy your ENTIRE iTunes FOLDER to an External Drive... and then from the External Drive to your New Computer..
Full Details Here > http://support.apple.com/kb/HT1751
An Added Bonus is that you will have a Backup of iTunes.
... Is there a way to maintain two accounts on one PC and prevent my wife's apps and music from going to my phone and vice versa?
Have a read here...
And See Here...
Basically... Create a User Account for each User... Then Each user will have their own iTunes library..