Regarding runneth - For a while, Viz was the champion of the archaic verb form, suggesting knowest on one occasion and endeth on another. I agreed with both of these proposals, and I think I probably mentioned, like Dave, Shakespeare and the King James Bible.
At a guess, I'd say the words of this type that were in our initial word list, YAWL, were those found in dictionaries, and they would be the irregular inflections, like dost, doth, hast and hath. Dictionaries probably don't list words like runneth because they're regular forms, whose meaning we're supposed to be able to work out for ourselves.
I wouldn't go so far as to say we should allow an est form and an eth form for every verb. Probably usage in literature is a fairly good guide.
It seems that runneth wasn't actually used by Shakespeare, but my speed reading of the King James Bible spotted 11 uses of the word, including "my cup runneth over" in Psalm 23. A full-text search on Project Gutenberg matched 381 books (although quite a few of these seemed to be works of Bible commentary).
So, I'd say runneth should be added to the list.
Regarding utero, I think Binkie and Dave are both right: it's only used in the phrase in utero, not as a word in its own right, and the phrase is generally flagged as an unassimilated (or un-naturalised) foreign one.
