So after a six month break from Oblivion I've finally got around to installing it on my new rig. I updated all my mods/Utilities and did the BOSS and Bash stuff, however on reading the BOSS log it had new recommendations for some mods, specifically that of TES4edit cleaning. I followed the link and read through it all along with the FO3edit guide, but i've a few queries.

On the wiki page it specifically says not to clean any of the mods that FCOM is dependent on because it can break stuff because of mod interdependencies, but if i don't use FCOM is it okay then to clean OOO? Also since i'm a complete noob at using TES4edit is automated cleaning enough or should i really spend more time learning to do manual edits as well? I have looked at some of the simplest mods in my modslist but i've a sinking feeling i couldn't spot a wild edit if it jumped up and down in front of me and then slapped me silly.

This should help: http://www.gamesas.com/index.php?/topic/1177151-list-tes4edit-cleaning-list/

Even if you arn't using Oscuro's as part of FCOM, cleaning it will break the mod.
The same applies for Mart's, WarCry - in spite of what may be written elsewhere - and Frans.

In terms of wild edits, I would say it depends on how much time you want to devote to learning - not just a few fundamentals, but the ins and outs of each mod individually. There's a cleaning guide http://tesalliance.org/forums/index.php?/tutorials/article/45-mod-cleaning-faq/, which you can use in conjunction with the cleaning list linked above. The guide can help you figure out what to clean.

In the mods that I've cleaned, most wild edits are either worldspace records (edits to the exterior world) in cells not intended to be used by the mod, or cell records (edits to interiors) in cells not intended to be used by the mod. So if you're cleaning a village mod, for example, and the village is located in the West Weald, but you see that worldspace records exist for cells in the Valus Mountains, those records might be wild edits. The only way to know for sure is to get to know the mod; play through it, or open it in the CS, to make sure the mod doesn't actually need any of those edits. But don't be afraid to experiment, as long as you make backups of the plugins and your saves.

The simple hard-and-fast rule here is that if a mod is on the Do Not Clean list, don't clean it. The only people who know what records are safe to clean are the people working on the mod, so any mod that is on the do not clean list is considered unsafe for the lay user to run a TES4Edit auto-cleaning on.