The Spirit Realm

I don't know of any such site, but there is a storyline that you can access from in-game or read it off the .txt files in your EQ directory. EQ's site used to be decent at telling a story when expansions came out, but it seems like it is less plot and more flash nowadays.

EQ lore is also pretty complex. There are exceptions, like LDoN, LoY, DoN, but for the most part, it would take an encyclopedia volume to cover the lore behind each expansion. Hell, there was enough going on back in Basic for more novels than one guy could write, I bet; the internal intrigues of Qeynos, Freeport, Neriak, and Erudin are each solidly deep for their own exploration. You want a retardedly complex task to take up some time in EQ? Try killing some old world quest NPCs and tracing why each has the faction hits that he does.

For older lore, look under Offisite > Turlo > Lore Library. This doesn't cover newer stuff, though, but is a compilation of all the 'books' in the game.

For newer stuff, yeah, the .pdf or .txt files in your EQ directory should cover the basics at least. For example: EQDOD_man_v5.pdf covers DoD history.

Or maybe a brief overview can be found at http://samanna.net/gen.info/lore.shtml