I own both Penumbra Fantasy Bestiary and the Monsternomicon.
I like both books, and have read both cover-to-cover (I'm wierd like that).
That said, I have to reccomend the Monsternomicon more. Why? It's a very good read, the art is fantastic, and the rules are relatively solid 3.0 (there's a few constructs with no Charisma [gr...] and something that gets a size penalty to initiative [huh?] but other than that, it's good). The creatures are all incredibly innovative, although there is a heavy steampunk tone to some, but not all, of them.
Penumbra Fantasy Bestiary, in my experience, is too much of a good thing. There are so many creatures in the book that there are invariably bland ones mixed in with the quality. A lot of bland ones, in my experience. Although there are a bunch of good ideas (I really like the sabaoth angels, for one thing), they're aren't enough to justify the massive cost. Also, the flavor text is printed on engraving-style backgrounds that induce headaches, and the book consistenly give iterative attacks to the natural weapons of creatures with high BAB (one of my personal pet peeves).
Just my two cents.
Demiurge out.