For most apps, it probably doesn't make a difference. Most apps are self-contained in the Applications directory. Once they start up, they make a directory for themselves under Library where they store their application specific information. If you are going to reinstall an application and want it to be more or less the same as it was before, you'll need both directories which you can only get from Time Machine. If you just want a clean install, then you can do either one and it won't make much of a difference. The exception that comes to mind for me is applications that you have to register. Since I don't know how each of them does their thing, you might have some trouble where you need to re-register the application. Check with the developers of the specific application for that one. Also, anything that doesn't get installed into the Applications directory (System Preference Panes, UNIX tools, etc.) probably don't fall under this 'easy' category, but you're pretty safe with anything that you did a simple drag and drop install.