As the sub-title says I am somewhat confused by all the different patch options available. I have been playing Fallout (GOTY) for some time now with a handful of mods, all of which went very well, and even when I started my latest play-through, this time with FWE, I have had a mostly bug-free game. I did recently encounter some serious bugs though and it made me realize that I know little about the best practice for building a stable platform in Fallout onto which to add mods and how to avoid conflicts between various mods. About the only thing I am sure on is that BOSS for FO3 is an absolute must to keep a good load order. Coming from Morrowind and Oblivion, the Unofficial Patch seemed a must, but the latest version of that is now over two years old, and I have recently read conflicting advise as to whether it should still be used at all. Additional bug-fixes have also recently popped up, only for some users to advise against using them as they add new bugs. So I would be grateful if someone could answer the following questions:
Is the Unofficial Patch still recommended or are there some setups (eg FWE) which incorporate/supersede its changes and therefore make it superfluous?
Are there further patches that should be installed in addition/instead of the Unofficial Patch (eg, Master Fix)?
Regarding the http://www.fallout3nexus.com/downloads/file.php?id=16665, I read that the Invisible Wall Remover part of it is problematic and in addition another of its components - http://www.fallout3nexus.com/downloads/file.php?id=16490 by Tommy - seems have been updated more recently than the Master Fix, would it be better to just use the Error Corrections (is it truly more up-to-date? does it have its own issues?) or use that on top of the Master Fix? Do they actually fix outright bugs, or is it more user preference (eg: hairs on ghouls - can it lead to crashes or does it just look nicer?) and performance enhancing/smoother FPS?
What about creating your own merged patches in FO3Edit, has that now been superseded by the Bashed Patch in Wrye Flash? If not what is the best practice for creating one, ie load all mods at once, or create several patches to remove problems between certain sets of mods only? Do I still need FOIP patches? Are there any mods that should not be included in a merged patch?
What about dirty mods? BOSS for FO3 does not currently include info on this, does that mean it is not an issue in Fallout, eg due to improvements in the Creation Kit? If it is an issue, how best to clean mods?
Finally, for Oblivion it is recommended to run Meshes through PyFFi, but I have seen no mention of this for Fallout, so is it recommended or can it lead to problems?
Sorry for all these questions, and many Thanks in advance for any answers!

The unofficial patch is not outdated. It fixes plenty of bugs that have not been fixed by the official patches and does not, generally speaking, cause crashes. There is ONLY ONE known crash, and there is a fix for that under the discussions tab at the mod's Nexus page. I don't know why that fix hasn't just been uploaded as a plugin, but it's there. I can't think of a good reason not to use the unofficial patch.

I posted in a recent thread about getting a performance improvement with the Master Fix, but I don't think that was related after all. I don't use the Master Fix, but I do the Error Corrections mod. I noticed some pretty serious problems with NPC pathing and animations after I started using it, but running master update and waiting for cells to reset fixed that problem.

Dirty mods are not a concern as far as I know, and PyFFI does not work with FO3.