I have a mac so not sure if iTunes if different in the PC version but I just have the 1 iTune account for myself and the other half's iTouch, you don't need different profiles.
When you plug in your phone/touch it pops up in the menu bar on the left. If you click on your phone icon it pops up in the main window about some general info plus a bar with your hard drive allocations to music, apps, movies, free space etc.
Along the top and within this main window there are some 'Tabs' - one of them is the Applications tab. If you click on this tab it shows all the applications you have downloaded into your iTunes - they each have little tick boxes next to them and all will be ticked by default.
Un-tick the apps you don't want and then hit the Sync button at the bottom.
Then plug in your other halfs iphone and go to the tab button again. All the applications will again be back to being ticked by default so repeat the process, un-tick the ones he doesn't want and Sync.
In future it will now remember each profile and will only sync the apps that are ticked. If you download any new apps in future they will automatically be ticked for both phones so if you don't want it you have to go back in to the tab again to take it off. It doesn't re-tick them if there's only an update though.
I also do this for chunky apps that I don't want to have stored full time on my phone like Lonely Planet or the Ikea Catalogue. They're sitting in my iTunes full time but only go on my phone when I need them.
I *think* that's all you need to do however I caveat this with the fact I'm going from memory and I don't have the best memory

If it doesn't work, shout, and I'll check it out when I'm back home tonight.