1: Aftermath by Al Steiner The story that introduced me to Storiesonline. I was reading it on ASSTR and saw the note pointing here. The story blew me away, as did the site. It's a totally adult look at an apocalypse situation in all it's horror, madness and hope.
2: Mike and Lily Naked in School by Don Lockwood Don Lockwood is the king of romantic teenage stories as far as I'm concerned. All are wonderful, and the whole Naked in School series is masterful. I just happen to like this episode the best - by a very slim margin.
3: Sea King by colt45 I'm a big sci-fi fan, and while there are many fantasy stories on this site that have all the things I like about the genre, this one has the kind of touch I relish - yes, there are bad guys and things get ugly occasionally, but it doesn't drag you down into the black hole others have. And, yes, I know many like it when things get very dark, but I prefer just a touch, not the sledgehammer approach.
4: Six-Months Turnaround by Morgan Morgan has a very strong series of stories in his Alison McGrath Universe that are fun to read and full of imaginative pieces. Yet it's this solo story about a young man taking over an old-line manufacturing facility and finding true love on the way that I read most often.
5: Thunder and Lightening by Lazlo Zalezac Yes, I'm a big fan of his Druid Universe. I also love his Crossroads Universe. In fact, I'm hard pressed to find a story of his I don't like. But like Morgan's stories, I find that this solo tale about a man who finds a way to change himself and betters both himself and all around him strikes a chord with me.