Would I mess up any of the quests in game, main, mages, etc. if I decided to go into the CS and make a couple of the NPC's essential so they will be around at the end of quests? There's a couple I would like to have survive just because I think they deserve to. For instance, Jauffre and/or Baurus depending on how I'm feeling at the moment. Thanks for any insight.

You'd be better of using the console command instead of a creating plugin for compatibility sake:

SetEssential BaseID #

So you'd have a look either in the CS or on the UESP for Baurus' BaseID, which is 00023F2A.

Then use the command

SetEssential 00023F2A 1

Which makes Baurus essential for your current character playthrough. This won't break anything, unless you make a character essential that gets force killed by a script, which could cause some issues in quests. These are listed here: http://www.uesp.net/wiki/Oblivion:Scripted_Deaths, so don't make them essential. Also be aware that some quests and scripts change the essential state on some characters (like the MQ for Baurus for example), so you may need to re-apply the command.

thanks so much for the info and the link, much appreciated

Another way to go about this (A way I prefer, because it gives you so many options for all different RPs/Scenarios) is to use http://www.tesnexus.com/downloads/file.php?id=20509

It adds a spell, so you can set any NPC as essential or not (along with some other options), whenever you want.