I can’t pick just one! How about a couple of favs?

Snuff– theprincessbee

It’s the Thought that Counts– Gladrial

The Villain – XMarisolX

Five Things That Never Happened to Harley Quinn– Risquesno

I think you can still find all these on fanfiction.net. Several (or all) of them also resided on jokerxharley.net which no longer exists, sadly.