Thank you for looking into this for me, but since I fixed my problem by simply deleting the old SDKs I’ve moved on.
However let me clarify exactly what was going on one more time, just in case you guys decide to pursue further.
I had the old 10.6 SDK in /Developer/SDKs, it could have been ‘special’ in that I did alot of weird things for a former project and I just don’t recall.
For the sake of explanation though lets say it wasn’t, what then?
I installed OSX Python 3.5.1, created a virtual environment using the pyvenv command from that newly installed Python 3.5.1, and sourced its bin/activate.
Then when running pip install ZODB, the compiler would be passed the -isysroot flag for the 10.6 SDK, which would change its include paths and it would find no includes or libs (if you sym link the includes into the include directory of the virtual env you will get farther and see that the linker does not find libs either). By suppling adding -v to CFLAGS you can have the compiler output the include paths and compiler call when running pip install. That is how I noticed the alternate system root supplied by the isysroot flag. Grepping around found me the _sysconfigdata.py file where that stuff was specified, it took a bit to realize that file came with the distribution and wasn’t generated on my system.
When not in a virtual environment, ZODB would install just fine into the system python (2.7).
Not sure why that is, or what would make the virtual environment different, but there you go.