Instrument Collections

Mugwumps: Michael Holmes has been an expert on unusual stringed instruments since the dawn of time. I send everyone who's question I can't answer to him. 
Frets.com: Frank Ford at Gryphon Stringed Instruments has been building this elaborate site since 1998. My favorite place is "the Museum" - where he's gathering high quality photos of lots of rare stuff that has come through his shop for repair. Tons of other instrument info also. 
Vintage Instruments Museum: Lowell Levinger's collection of rare fretted strings.
Rainer Krause Collection of Antique Guitars - Rare - Curious Musical Instruments (a new web site, with more to come. The name says it all!)
National Music Museum: America's Shrine to Music on the Campus of The University of South Dakota. The largest collection in the States.
Atlas of Plucked Instruments: Collector Henny de Bruin has created a one-stop Atlas for all fretted plucked stringed instruments of the world. Photos, text, and often, tunings provided.

Harp Guitars

Harpguitars.net: Simply THE Internet source. And I should know....
Knutsen Hawaiian and Harp Guitars: The late Dan Most and his partner Tom Noe's published the first and only book on Knutsen's harp guitars, along with his and other's "Weissenborn-style" Hawaiian guitars.
The Knutsen Archives: My own specialty site which takes up where the book leaves off, cataloging the instruments of Chris Knutsen, now part of Harpguitars.net.
Larsons Creations: Not just harp guitars, but all the instruments built by the fabled Larson Brothers. By the expert on the subject, Robert C. Hartman.
Stephen Bennett: Stephen, a fellow harp guitar player, is a great guy, a new friend, and an incredible guitar player. If you like instrumental acoustic guitar, buy his CDs!; and if you're interested in harp guitar, he's the best of us!
John Doan: John has been doing a similar presentation to mine (though without all the silliness) for years. His main instrument is the harp guitar and he collects (and often uses) many of the same antique zithers, banjos, etc. that I do on his several recordings.

Guitars

EarlyRomanticGuitar.com: This is wonderful site full of photos and valuable information on early guitars.
Tenorguitar.com: You guessed it - some guys who apparently can't play six strings are devoting some serious web space to this under-appreciated instrument. 
Vintage Guitar Magazine: Go buy their mag/newspaper. Every vintage dealer in the states advertises in there.
20th Century Guitar: The other main vintage guitar source. Now at your newsstand.
Guitar Notes: One of the many links sites for the guitar.

Mandolins

Howe-Orme Mandolinettos: My study of these infamous instruments.
And More Mandolinettos: My expanding page on the many makers and varities of the "guitar-shaped mandolins."
Mandolin Cafe: I don't know this guy, but lots of great news and links to the mando world.
Mandozine: Another great looking mandolin site.

Zithers

A note about Fretless Zithers: HUNDREDS OF THOUSANDS of these were produced and sold, and I understand that 99% of you who found me naturally have a question on your "treasure."  I love these as well - however, they have very little value.  If you MUST know the value, check eBay once a week and you will likely find yours or one similar.  If you want it restored, it is not worth the money.  If you want to re-string and play it, see here.  Note that both Kelly Williams of the Guitar Zither Clearinghouse and Garry Harrison of FretlessZithers.com have both retired, and until their sites hosting plans lapse, remain the best and only source of information on the topic. I have updated my own page to incorporate the latest news and some of Kelly's important work. I would consider this article essential and a good place to start.

Zitherist International: Donald Tsusaki has created a site that should offer a lot of  potential on various aspects of all the zithers.
FretlessZithers.com: NOTE: Garry sadly passed away on 9/4/2012. Garry Harrison created a spectacular site for these wonderful, ubiquitous instruments. I'm thrilled that he chose to promote the new term presented by myself and Kelly Williams (see next).  Garry retired his entire collection to the Phoenix music museum. UPDATE March 2015: Garry's family has re-posted the entire web site!
Guitar Zither Clearinghouse: Kelly Williams, who has now retired, was one of the world authorities on fretless zithers.
Bob's Ukelin Home: Another passionate eccentric who focuses on the lowly, albeit essential, ukelin.

Stoessel Lutes: My extensive page on these now-forgotten hybrid instruments from Germany, and possibly the world's only information in English. Marvelous instruments!

Ukes

Flea Market Music, Inc.: Jim Beloff is the local ukulele expert, and his site serves as an open forum for uke-buffs everywhere.
Altpeter Double Bass Ukulele: My page on this incredibly bizarre uke!

Luthiers

Kerry Char finally has his web site up. Kerry repairs nearly all of my instruments and built my custom Miner-cello and resophonic guitar seen on my site.

Dealers

Players Vintage Instruments. Collector Lowell Levinger always has a wide variety of rare, cool stuff.
Elderly Instruments: I've gotten vintage instruments, strings and accessories, and hard-to-find CDs from them - all at the best possible prices. Run by Stan Werbin, a long-time collector and great guy.
Bernunzio Vintage Instruments: I've gotten several instruments from John Bernunzio. He's been around for ages and always has the best selection of the more obscure banjos, ukes, etc.
Mandolin Bros.: The best vintage stringed instrument store around. These guys have an undeserved reputation for being top-dollar. They're really not. It only seems that way because all of their stuff is the best possible quality. Stan even gave me a deal on my fabulous 3-point F4.
Gruhn Guitars: A ton of inventory, helpful staff, expert identification - I've gotten a couple of my better pieces from them.