Unique exlusions for numerous servers

I was wondering how people handle exclusions for servers when you have a number of servers that all have unique exclusion requirements.  So in my environment I've got 100 or so physical Linux servers; all of those share some basic Linux exclusions, but then probably 30 of those are running different applications that all have their own unique exclusions that aren't related to other servers, so one server may exclude /etc/customapp1 and another /opt/custom app2 and some have multiple directories that need excluding that are only unique to that server.

So, is there a best practice or just personal preference?  I know technically you can add all of those exclusions to one dataset, the only thing I've seen I don't like about that is all the exclusions are in one big list and it ends up being hard to see which exclusions belong to which server and with 30 servers with multiple exclusions, you end up with one big list.  The other way would be to create separate datasets for each app needing custom exclusions, which you end up with a lot of data sets.  The other way I've seen mentioned is using an avtar.cmd file, which I guess you'd only know what's there by checking each server, though with TSM we're using now that's how it is I suppose.

Anyways, any tips/thoughts would be greatly appreciated.