The Weatherlight Saga
The longest, most well known story arc so far is the Weatherlight Saga. It contains the Artifacts Cycle, the Masquerade cycle, the Invasion cycle and the book Rath and Storm.
This is the order in which the books where released, and the order in which I would read them.

Rath and Storm by Peter Archer
The Brother's War Jeff Grubb
Planeswalker by Lynn Abbey
Time Streams by J. Robert King
Bloodlines by Loren L. Coleman
Mercadian Masques by Francis Lebaron
Nemesis by Paul B. Thompson
Prophecy by Vance Moore
The Thran by J. Robert King
Invasion by J. Robert King
Planeshift by J. Robert King
Apocalypse by J. Robert King

This is not the chronological order though. The chronological order goes like this:

The Thran
The Brother's War
Planeswalker
Time Streams
Bloodlines
Rath and Storm
Mercadian Masques
Nemesis
Prophecy
Invasion 
Planeshift
Apocalypse

The argument for reading the books in chronological order is that it's easier to understand as some questions are answered right away. The argument against it is that those questions keep a cool mysterious vibe. It's really up to you which order you take: if you go for the mystery, read the books in the order they were released. If you don't care about the mystery, read them in chronological order.

Generally storyline fans consider the Brother's War a very good novel that is also a perfectly fine read on its own. Prophecy is generally considered utter dross and pretty much every storyline fan will agree that you're better of getting a summary of the internet than spending time actually reading it.