OK, this one is really stupid. Easy Booking Service says not to link to its home page; instead, it wants you to read the linking instructions on this page, which sends you to this page, which contains a form to fill out, and you'll supposedly receive the URL by e-mail.  DES permalink

Alistair Fraser's Bozo Filter permits you to specify URLs from which links to your web page are not permitted. (Click here to see it in action.)  DES permalink

Manpower prohibits all links to its site without express written permission. Another candidate for the Hall of Cluelessness.  DES permalink

DKSystems has one of the dumbest linking policies I've ever seen: "You may refer to the URL of this Web Site without limitation, but you may not link to this Web Site without the prior written approval of DKSystems." You'd think that a software development company would understand how the web works, wouldn't you? (There seem to be a few hundred web sites that link to DKSystems, according to the major search engines; I wonder if all of them really asked for permission first.)  . . .  UPDATE: A Google search reveals that several other sites have linking policies that are very similar to DKSystems' policy. ("Gee, this sounds good, I think I'll copy it for my site.") That doesn't make the policy any less ridiculous, but these sites all deserve to share in the ridicule: Avfuel; Aztek Solutions; Chicago Interactive Marketing Association; Denmark Tours; e-guana.net, Inc.; FindHomesPlus.com; Freestyler Network; GorilLAN; HireSmart; Hooked on Phonics; Interim Services, Inc.; LionArt Productions; Market Results; MSX International; Project Leadership Associates; Pulse Systems; SEEK, Incorporated; Spherion (also here and here); Superior Group; Webauthor.com; and Yoshinoya USA. (Consider this list a "who's who" of utter cluelessness.)  DES permalink

Crossrail (U.K.), Cystic Fibrosis Network, PremiumTickets.com, and Riverstone Networks all prohibit deep links. Equipped To Survive prohibits deep links from commercial sites. ConvenienceWorks prohibits deep links as well as links to its home page from sites that it does not consider "suitable." SpotLife requires express written consent for deep links, and prohibits links to its home page from web pages that contain content that is not appropriate for all age groups.
Update (Sept. 8): Riverstone Networks has revised its linking policy -- it now invites other sites to link to any pages they care to. Another victory for the Internet and common sense!  DES permalink

Matsushita Group and several of its divisions (including Panasonic AVC, Kyushu Matsushita Electric, Matsushita Electronic Instruments, and Matsushita Inter-Techno) require linking sites to contact Matsushita's web administrator before linking, and again each time a major change is made to a linking page; deep links are not permitted.  DES permalink

BreakTV.com requires other sites to request permission before linking to it, and permits links only to specified pages.   DES permalink

Here are some more sites that prohibit deep links: American Society of Travel Agents, Autodesk, Autotoys, Mars Inc., and Oasis Studios.  DES permalink

PinkSheets LLC requires sites that link to it to fill out a registration form and agree to detailed terms and conditions.  DES permalink

MBD2.com requires sites that contain more than three links to its site (e.g., 1, 2, 3, 4) to obtain permission first.  DES permalink

The American Society for Clinical Pathology requires organizations that do not fall within specified categories to obtain permission before linking to its web site.  DES permalink

TRUST International Hotel Reservation Services prohibits deep links to its web site.  DES permalink

The Smithsonian Institution's Hirshhorn Museum and Sculpture Garden and National Postal Museum both prohibit deep links.  DES permalink

Martindale-Hubbell prohibits deep links to its site without specific permission, requires notification of links to its home page, and claims the right to have links removed upon request.  DES permalink

SHAZAM, a regional ATM network, requires other sites to obtain permission before linking to its web site, and requires that its logo be included next to the link.  DES permalink

News International Group prohibits deep links to its sites, including The Times and The Sun, without express written permission.  DES permalink

Bloomberg.com claims that by linking to its site, you agree to be bound by its "Linking and Framing Terms and Conditions," a detailed list of restrictions that Bloomberg reserves the right to modify at any time. Among other things, it requires advance permission for deep links, and requires you to fill out a registration form before linking to Bloomberg's home page.  DES permalink

Certegy Inc. prohibits deep links and imposes all sorts of other restrictions on links to its home page -- for example, links are not permitted from any web site that "contains material or content that may be considered objectionable," including "sites that promote controversial social or political ideas." Certegy says it can revoke the right to link to its home page at any time.  DES permalink

Texas Instruments imposes a set of guidelines on sites that link to its site; one guideline states that linking sites "should not contain content that could be construed as distasteful, offensive or controversial."  DES permalink

Michigan.gov (the state's official web site) permits other sites to link to it "under limited conditions," and asks to be notified whenever a link is created.  DES permalink

Telecom New Zealand's site says "In accordance with Internet protocol, we require that you request the permission of Telecom to link to this site." They must mean "upside-down Internet protocol."   DES permalink

CIBA Vision, KatSpace, Legalresearch.org, and TAPPI all prohibit deep links to their sites.   DES permalink