Well, I don't know about slashy, shippy stories, which seems to be the norm for fanfics these days, but the Orion Press Archives (http://www.fastcopyinc.com/orionpress/archives.htm) have a TON of well-written, long, plotted and brilliant fanfic, interspersed into the whole of the series, the movies, and even beyond.

Also, if you're interested and you live in the US, cbs.com has all the episodes of all three seasons of the original Star Trek series online to view at leisure.