http://www.fanfiction.net/s/3428015/1/
The Trouble with Timelines by Fizzy 13, last updated 04/04/07. Unfinished, but good.
http://www.fanfiction.net/s/3473292/1/
Enigma by KyonxHaruhi, one-shot. Thoughts running through Haruhi's mind. Pairing obvious.
http://www.fanfiction.net/s/3413734/1/
The Death of Haruhi Suzumiya by Turbanator. Last updated 03/30/07. Also good, and I'm not saying that just because Haruhi's dying. Plot summary: Haruhi's dying.
http://www.fanfiction.net/s/3464468/1/
Ghosts of the past by KyonxHaruhi. One-shot. Ummm, something about ghosts. Pairing also obvious.
http://www.fanfiction.net/s/3424053/1/
Sliders, Demons, etc by Deus X Machina
A series of sorts, so there's less continuity between the "episodes", though there is continuity. Last updated 03/29/07.
http://www.fanfiction.net/s/3462643/1/
First Kiss by Saiyume. One-shot. Kyon/Haruhi.
http://www.fanfiction.net/s/3460908/1/
Documentary by drunkdragon. One-shot. Kyon/Haruhi. I'm beginning to see a pattern here.
To recap, All of the SHnY fanfiction I've seen that pairs Kyon up with somebody pairs him up with Haruhi, except for one that pairs him up with Yuki (listed above), and one that pairs him up with Mikuru, but that one's sort of mediocre, so I didn't list it.