Heroes of Battle and the Miniatures Handbook. I have been converting some monsters from time to time from FF and MM1-V. I have also consulted Lords of Madness, and Libris Mortis for that purpose, too.
I agree with the Auld Grump that Dave Noonan's Heroes of Battle is still a go-to book for me. Of all of the late era 3.5 hardcovers, Heroes of Battle was the most innovative and most under-appreciated DM focused book for 3.5 that WotC released. If you can find it? BUY IT.
Now, all that said -- that's just me. I have a frikkin RAFT of 3.xx hardcovers I am not using. Hell, I NEVER used them, to be completely honest. I got rather silly with my "Compleatist" shopping habits as the 3.x product line moved forward during its cycle. Funny thing was, I rarely read them. It was a collection/pride of ownership thing.
In truth, the more I had of it, the more I came to realize that all these books were utterly breaking my 3.5 Age of Worms campaign at the time. Indeed, one of the major attractions to me at the time PFRPG was released was it was a way for me to stop using ANY 3.5 material. For a time, I did exactly that, too.
But for all of that, I think that the most important thing to remember is that you CAN use any of those books that you care to -- many of them without any modification at all.
Whether or not that is a terribly wise thing to do is another matter. In the end, a GM decides what they want to use and what they don't. I think one of the strongest aspects of Pathfinder RPG has been that a gamer can pick and choose from among their 3.xx library concerning what they want to use in their Pathfinder game.
There is no right or wrong answer here. If you like it and your players like it and you find it makes gaming with Pathfinder RPG fun for you? Then that's just AWESOME.