I'd say the joy of reading His Dark Materials was not knowing what exactly was going to happen next. If you asked someone to describe what it's about, that person would find it fairly difficult to summarise in a line or 2.
I quite enjoyed Dark Materials, especially Northern Lights (aka Golden Compass outside the UK). I'm not sure if I'd put it as my top book, but I'd rate it pretty highly. The alethiometer's one of the best story telling devices I've seen in any story period.
Pullman has an uncanny ability of being able to drip feed the reader bits of the story leaving him/her puzzling over the next piece of the puzzle. Each chapter (especially at the beginning of Northern Lights) manages to answer some of the questions, but the answers just dig you deeper and deeper into the mystery wondering what it's all leading up to.
I was wondering about the series thing, but I guess you could argue that in the prologue to LOTR, it says that it's all meant to be one book. At the beginning of Northern Lights, it says pretty much the same thing. Harry Potter can't really be judged as a series yet- it's not finished, so how can you call the series one of the nation's best loved books if you don't know how it's going to end- for all you know books 6 and 7 may be rubbish, leaving the BBC looking stupid. Also loosely connected books eg Pratchett's Discworld are often considered separately (or at least as the Death series, city watch series, witches series etc, but that could have gotten very confusing. The BBC had to strike a balance, and whatever they came up with was always going to be contraversial.