My Unfinished Stuff:

The Poker Hand Series - A detailed look into Jack's past (updated: 5/19/02)
Don't Know Jack - Nobody really know Jack, least of all, Jack (updated: 5/1/02)
The Will of Jack - Will Tippin's thoughts about his kidnapping and kidnapper (updated: 5/1/02)
Jack of All Trades - Abby investigates Will's disappearance (updated:5/10/02)
Jack Be Nimble - Jack faces the consequences of his latest 'off the book' instance (updated: 5/16/02)

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Other Fanfic:

Credit Dauphine - No doubt it's my Jack-preference showing, but I highly recommend "_____" and "The House that Jack Built" from this archive.
Fanfiction.net - There are some good ones here and there are some really bad ones. And there's a lot, with more coming nearly every day.

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Alias Links:

Credit Dauphine Writer's Resource - Info and Links about the show
Alias-Online - Episode Summaries and Transcripts, other stuff
SD-6.com - Alias Info, Plot Synopsis, etc.
ABC Website - Official Website