Disclaimer: When I think of "layout" I think of "Visual Appeal" as well as "Ease of Use" - it needs to be interesting enough for me to stay interested but simple and uncluttered enough for me to find what I'm looking for. In other words, I want a layout that's not cluttered, but is not sterile either.
Bad Axe Games does it for me. When I think "great layout" I think of the HoHF series. I also like the layout of the FFG books, though sometimes the amount of white space is a bit excessive.
And while it may start a heated debate, I hate to say it, but Malhavoc probably rates among the WORST layouts for me. For lack of a better way of putting it, Malhavoc's layout is too clean - to the point of being sterilized and positively bland. I have a very hard time keeping my attention on the page because of the intense visual sameness. In my opinion, they've swung the pendulum too far on "clean layouts" to the point where the visual blandness keeps me from being able to read their books... which is too bad, since I really enjoyed the original PDF layouts of the Book of Eldritch Might I and II (the ones done before they settled upon their current signature style).
Malladin's Gate (in PDF) does nice clean work, but sometimes can run slightly to the "too clean" side as well.
--The Sigil