No time to explain, but logged in to list

Distress
Axiomatic (story collection)
Luminous (story collection)
Permutation City
Quarantine
Diaspora
Zendegi
Teranesia
Orthogonal trilogy
Schild's Ladder
Incandescence

I haven't read many. I fully recommend Diaspora and Luminous (short story collection), I was less sold on Permutation City.

This should be fun!

Distress - it's like the kitchen sink of hard/near-future SF

Quarantine - very enjoyable, but a bit simple-minded

Incandescence - seems like a return to early Egan's minimalism

Permutation City - cool, but rather off for me

Schild's Ladder - doesn't feel innovative, the ending has the same vibe as that of Permutation

Zendegi - was expecting more LW mockery after the discussions, unfortunately it was very limited

Diaspora - although brilliant in some respects, very confusingly written

Teranesia - just boring, I understand why it's not so known

Haven't read yet An Unusual Angle; the Orthogonal trilogy I'll read when I get it whole.

Haven't read them all. Of the ones I've read:

Axiomatic (best, collection of short stories)

Permutation City

Distress (contains 'sufficiently advanced' biotechnology that amazingly did not piss me off)

Diaspora

<Edge of what I'd wholeheartedly recommend>

Schild's Ladder

Incandescence

Quarantine (I found it nearly unreadable)

I suspect he's one of those authors that everyone agrees one of his books is great but nobody can agree on which one...

EDIT: I find myself seriously considering the possibility that Diaspora is in the future of Permutation City...

Diaspora
Distress
Quarantine

I haven't read the short story collections close enough together to rank them, but I'd generally recommend them

Permutation City
Zendegi
Schild's Ladder
Teranesia

Didn't finish (more physics than I could appreciate)

The Clockwork Rocket
Incandescence

If you liked Diaspora, you'll like Schild's Ladder. Zendegi is more psychological and a different kind of fiction, thus not much of my favourite.

Incandescence and Orthogonal should be grouped together; not bad, but different, and IMHO Orthogonal suffers from being a trilogy. They are also much more maths-heavy.