I’m a big fan of both Atlas specifically and monster books generally, but I still really can’t recommend the Penumbra Fantasy Bestiary. Oh, it's got some good points – it's big, includes a great set of indices, provides neat adventure hooks for every monster, and clearly delineates between open and closed content. And did I mention it was big?
But the book is really expensive, the art is only OK, the rule implementations are only adequate, the flavor text sections are hard to read, and it uses 3.0 rules. These are drags, but not outright deal killers.
My two big problems are (1) as a whole, this monster collection has a scattershot feel, which is probably due to the numerous contributors, and (2) the book has way too many cutesy or gimmicky monsters for my tastes. On the other hand, if you like tinker gnomes, or run a high-fantasy, heavy role-playing game, you may very well love the Bestiary.
Have you considered the Tome of Horrors? It’s probably the non-core monster book that gets the most use in my campaign.