If you're looking for a list of fanzines by fandom, this is what I have so far:
Place of Honor: Starsky & Hutch. Pepper has compiled the most amazing and complete fanzine listing. Mahvelous. Go here
1. Alphabetical listing
A-Team - list here (last updated in 1997) and here
Beauty & the Beast here and here
Buffy and Angel
Blake's 7 - Judith has an extensive list here
Dr Who - partial lists available here and here and here
Due South -Ray Vecchio Fanzines and Ray Kowalski Fanzines
Inspector Morse here
The Magnificent 7 here
The Man From U.N.C.L.E - slash fanzines here, gen and slash fanzines here
The Professionals -The Hatstand and Palely Loitering (with their own LJ here)
Quantum Leap - old list, needs updating
Rat Patrol - Excel spreadsheet here
Real Ghostbusters - here (defunct, last updated 2002). A more current list is here
Robin of Sherwood here
Seaquest here and here
The Sentinel - Loft Library -Slash Zines and Gen Zines
Shadow Chasers here (old archive)
Sherlock Holmes here
Stargate SG1 - old list here
Starsky & Hutch - Pepper's Amazing List With Every Possible Combination Except Pepperoni
Star Trek - K/S Slash Zines and Star Trek Zinedex (gen/het/slash). An index of stories published in fanzines by title and author can be downloaded from the KirkSpockCentral mailing list (membership required).
Star Wars - Star Wars Collector's Bible (older list archived here)
Supernatural - here
Voyage to the Bottom of the Sea here
Xena/Hercules - partial list here
2. Multi-Fandom Lists
Ming's Fanzine Archives (Star Trek, Star Wars & other Fandoms - click on the pdfs for the list)
Fandom Wikis - FanLore and Fan History
3. What To Do With That Aging Fanzine Collection? If you don't want to sell your fanzines on eBay or at a convention, the Fan Culture Preservation Project will help fans find homes for their fanzine collections - either at the University of Iowa or via fellow fans. More here and here.
What I like about the Fan Culture Project is that the University will pay for shipping and loading of the zines. I have several friends whose health has declined, don't want to sell their collection, but want to find their fanzines a good home.
Other places to buy/sell your fanzines: the Zinelist Announcements List, its sister discussion mailing list Zinelist or the SlashSwap mailing list. You can offer your fanzines on LJ at Fandom Swap. Jim and Melody Rondeau will also agent your fanzines online and at conventions for a small commission. As a last resort head over to eBay but beware you may be charged 2-3x more than you would buying from fannish sources.
For new zines/in print zines only: The Zine listing communities - one here on Dreamwidth and the mirror here on LJ. Melody Clark has started MediaFen, a fanzine listing blog. The RSS feed for LJ users is here. The direct blog link is here.
If you're trying to track down a fanzine producer whose website has moved or gone away, try using the Wayback Machine. Ex: The Zine Zone (last updated in 2003) is archived here.
Looking for Fanzine lists:
Buffy/Angel - some zines listed on Fanlore
Highlander - some zines listed on Fanlore
X-Files - some zines listed on Fanlore
5. Wanna Know How Your Ancestors Produced Their Fan Fiction?
Read "Fandom Before Computers"