Check out my http://www.gamesas.com/index.php?/topic/1232576-complete-modded-oblivion-installation-guide/ for how I use WAC and OWC-ND together.
Recent discoveries:
WAC - TCOS and TCOS Shops is something I have decided to stop using. Personally I feel that the weapons it adds (and their accessibility) overshadows the weapon balancing scheme in OWC-ND and makes some of the tiers obselete, plus there are plenty of weapon and armor varieties in OWC-ND anyway.
Enhanced Economy works fine with OWC-ND and I would highly recommend it over OWC-ND's economy.
Oblivion XP so far has been fairly good, I have not found any high level NPCs that were TOO easy (i.e. cheap exp) yet.
I seem to have an issue with some races with racial bonuses (i.e. Secret Elf mainly) that have skill racial bonuses that do not get applied after selecting class (note: these are actually passive abilities and not the base skill differences of a race). There has been no bug fix and I have not heard anyone comment on it yet in either of the OWC-ND threads, however there might of been something on the german ones. Basicly, I just player.setav to fix it AFTER selecting class. Granted, Secret Elf bonuses are a bit overpowered, +35 athletics and +15 marksman (on top of race base bonuses already). Perhaps someone should write a fix converting these to BASE bonuses?
However, Darnified UI and Alternative Beginnings also work fine, just delete the Menus folder from your temp folder before copying it over.
Otherwise, it's so far my favourite overhaul configuration, if you have any specific questions, pretty much everything I use is listed on that guide. I think I forgot to update a few, Cava Obscura works fine, and most recently I've started using Duke Patrick's Melee Combat, which also works fine.
Almost forgot, I wouldn't recommend using SM_SigilStone or any Sigil Stone rebalance. OWC-ND comes with it's own which I feel is nicely balanced.
One more thing about balance, Marksman is very strong in OWC-ND, it is comparable to FCOM_Archery tweaks and then some. I would recommend using http://www.tesnexus.com/downloads/file.php?id=32651 to remove the knockback effect from arrows and in general it has some combat tweaks that are highly recommended but in this case I make special note of this because some of the creatures are just too slow in OWC-ND and WAC.