Time Machine backup on per app basis with application preferences?
The short answer to your question is 'it depends on the app'. This thread in the Apple Discussions Forums implies that, at least for basic apps that do not have complex connections with the system, it is possible to restore via Time Machine. 

If I am not mistaken, Time Machine works the same way in all folders (including Library and Applications) as long as they are not listed as an exception in System Preferences. What this means is that if you open a new Finder window showing the user's Library folder and then call Time Machine, that should bring back the preferences subfolder for your app when you "go back in time" to when you had it installed. Naturally, you would have to know in advance the name and location of the app's preferences folder within your user's Library folder. 

After that is done, then opening Time Machine in a Finder window showing the Applications folder should bring back your app if you "go back in time" to when you had it installed. It's a two step process, but I don't see why it would not work at least for simple apps.