Hi Jon,
It's a bit of a difficult one here. Some different programs need different files to have different permissions. From my most recent install of something like this, I know Joomla (a CMS) has to have certain files with certain permissions to work correctly. This was all outlined in the install info which came with it.
Generally, if something you've installed doesn't work properly, check the permissions. If it works fine, I wouldn't worry too much about it. One final word of warning on that though, try not to leave anything writeable which shouldn't be writable and things like that...
I know that's a bit of a round about answer but permissions depend on the individual thing you are trying to run.
Jonathan
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