It's sort of impossible to answer because how can you compare where there's no common ground? I love the Hitchhiker's Guide series, but then I prefer the radio series slightly to the books, and then there's questions of which is the canon etc etc...
Or take His Dark Materials: I don't care for The Amber Spyglass much but my love for the first book Northern Lights is so overpowering is still balances out as one of my favourite series' (and I'm also very fond of books 2, The Subtle Knife). Proportionally, therefore, I love two thirds of HDM. I probably love (LOVE rather than just really-really-like) about two thirds of Discworld. So proportionally - about the same. But whereas two thirds of HDM means two books, that's like 26 books from Discworld. It doesn't seem a fair comparison... it's like trying to decide if you like Buffy The Vampire Slayer of Firefly better.
And then there's stuff that just doesn't seem compatible because the material is so different - how can I compare Discworld to the Philip Marlowe books or the Sherlock Holmes stories and say which I love the best? They just offer a completely different experience.
But if you held a gonne to my head for an answer I guess I'd have to say yes; Discworld is my favourite series.