Well, I don't know much about databases; but I will give one silly opinion...
The thing is I have been trying to learn various things available within Python...one of those things I run into was, precisely, HDF5. When I read about HDF5, I understood that it was a storage scheme and not necessarily a database (i.e., there is no database server running with its own intelligence to answer queries or return sets or anything like that).
Of the other two choices that you mention, I just quickly read the main webpages and it looks like MonoDB is a real database (requires a server) and Kyoto Cabinet does not, this last, again, it's just a storage scheme.
So, my first opinion, if you need speed, is to forget about using a real database and stick to a storage scheme...so, Kyoto or HDF5.
It seems Kyoto talks about one key,value per line...does not seem too impressive as a storage scheme...but maybe that's where speed comes from.
HDF5, from what I remember, is actually rather versatile as far as as to what it can store.
The Kyoto site does not look like much...how popular is this?
Just becauss I learned about HDF5 before I ever heard about Kyoto, it sounds like HDF5 is more popular within the scientific/engineering community...
Anyway, that's my un-educated opinion.
gsal