These are taken straigt from my personal bookmarks. Be sure to check these sites' link pages too, so you can find even more wonderful sites for The West Wing goodness!
The Icon's West Wing Fan Fiction Archive
The Jo & Ryo Collective | West Wing Fanfiction
josh and donna fan fiction by bramble
The Stickey Wicket (Fan fiction by Macha)
Christine's West Wing Fanfiction
Ballynihinch's West Wing Fan fiction
Suzy's All Things West Wing Page
coffee, beer, & redlights (mdrgrl1's fan fiction)
Distinctive Penmanship: fan fiction
Smiles, Tears, & Happy Endings Fan Fiction
Llorin's West Wing Fan Fiction
Coffeeplease's Fan Fiction Listing
Backpack Tales - West Wing Fan Fiction
Yahoo! JoshDonnaFF List (From there you can get to the "sister lists.")
Denial :: Josh & Donna's Index at Romantic's Garden
The White House Communications Office (West Wing episode transcripts)
Political Affairs (transcripts of all Josh/Donna scenes from the series)
The West Wing Unofficial Continuity Guide
West Wing page at Television Without Pity
Screenmusings.net ~ The West Wing Collection (episode screencaps)
My Serendipity (fan videos, episode clips, and a video history of Josh & Donna's relationship)
Dimples and Distinctive Penmanship Style Home | jenniellamb.com