I've read and enjoyed a lot of Clarke, but looking back on his works, I would rate the vast majority more highly in terms of influence than actual quality.
Foundation was fun, but underwhelming after having read the
Dune series, and
Childhood's End was full of great ideas, but they were somewhat clumsily and superficially explored. When I look at what Kubrick did with
2001 or even what Stephen Baxter did in the recent
Time Odyssey books (or Greg Bear rehashing
Rama in his
Eon books), it seems obvious that Clarke's ideas had a lot more potential than he was capable of realizing as an artist. His influence was vast and deserves recognition, but I can't in good conscience elevate any of his individual works above the better efforts they inspired.
Granted, I haven't read the apparent crowd favorite,
The City and the Stars--added to my list

My current Clarke favorite is
Songs of Distant Earth, though I thoroughly enjoyed the
Time Odyssey collaboration.
I can't do "best of all time," but the works that have impacted me most, as a teen:
Blood Music
Brave New World
The Positronic Man
Cat's Cradle (borderline sci-fi, but entrenched like a Pashtun on that border)
As an adult:
Anathem
"Repent Harlequin!" Said the Ticktockman (a short story, I know)
God Emperor of Dune (to pick one,
Dune Messiah is also right up there)
And for something less serious, David Brin's
Uplift series deserves mention, particularly the second trilogy centering on the planet Jijo, which can essentially be taken as one work. For uproarious, absurdist sci-fi, I'll take
Uplift over
Hitchhiker.