I love monster books. Love 'em to pieces (not literally - I'm horribly anal retentive about my books... but I digress).
That said, I like the Monsternomicon MUCH more than the Penumbra book. I haven't been able to bring myself to buy the Bestiary for my personal collection, even though one of my customers swears its a great book. It just kinda leaves me cold.
Sure there are more critters in the Bestiary, but they don't really seem to have a thematic link. The shear bulk, I think, dilutes the effect of the whole and leaves it seeming like an almost random conglomeration of beasties. From the multiple cursory looks through the book I've made (while contemplating removing it from my store shelves and adding it to my personal shelves), it also seems to vary greatly in quality from monster to monster (in the art, the game mechanics, and the usability of creature).
The Monsternomicon is the opposite of the Bestiary, at least as far as the things I've just described as not liking. I enjoy the style of art in the Monsternomicon a great deal (that doesn't make it better, I guess, just that it's more appealing to me); I appreciate the "take" on fantasy embodied in the Iron Kingdoms more than Penumbra (at least as far as I'm familiar with both - which is kinda hard for IK, since there isn't much available just yet).
And I'm prattling on...
For me, while the Monsternomicon may have fewer creatures in it, it has a much greater number of creatures I can use than does the Penumbra Bestiary. Which one is more useful to you depends more on what type of fantasy you like, and what kind of campaign you run.