I am looking for any information on the Microsoft TFS Web Services. First I know accessing the Microsoft TFS Web Services directly is not supported and Microsoft provides no
There is good documentation now: https://www.visualstudio.com/integrate/get-started/rest/basics
I'm not aware of any documentation for the TFS web services, but I can share some tips on calling them.
The NTLM authentication you mention is really a separate layer: you must authenticate to IIS before it lets you call TFS web services. I'm not aware of any Open Source software that will do NTLM auth for you, but TFS 2010 makes it easy to enable "Negotiate" authentication (SPNEGO on Wikipedia, Authentication by using Kerberos Ticket on MSDN). Negotiate supports both NTLM and Kerberos subsystems, and there may be some existing software you can use to drive it using the system's Kerberos libraries (I think curl does it). If you had to build it yourself, it would probably be easier to go the Negotiate-with-Kerberos route.
Once you're authenticated, you can start calling services. Start by pulling down the WSDL for each service (stick a "?wsdl" suffix on each endpoint URI). Hop over to where TFS is installed and explore the web application directory for endpoints. There are several versions of some endpoints for back compat with TFS 2005 and 2008, but usually new versions are not redundant (they add new stuff). You might have a favorite SOAP client library already (there are many for Java), but I can't really recommend any because we wrote our own at Teamprise.
Services like version control, build, and common structure are easy to discover via WSDL. Most the operations have obvious names, but the complex type fields are often super-abbreviated. The best way to figure which methods to call when is to watch the VS TFS client or TEE with Fiddler or Wireshark or some other HTTP inspection program. TFS VC does do things like file uploads/downloads outside the web services (watch a network trace to see the multi-part MIME upload process and be sure you're sending the right values if you implement this).
A note of caution on the work item tracking web service: this one is going to be extremely hard to master. The WIT design involves the client pre-querying the server for large amounts of schema-less metadata, which is saved on the client (but refreshed incrementally as more web service calls are made). This metadata drives all the client side behavior about work items (what fields are in a work item type, the type of a field, which values are allowed in fields, the rules that run when they change, etc.) and it will take a long time and serious study to build the client behavior to bring a work item to life. Once you have a work item, sending it to the server for update via web services is easy.
It's a lot of work, but it's possible to do incrementally, for example, if you only need some VC features. The TEE team is working on making access from other platforms easier. Please contact Martin Woodward (martin.woodward@microsoft.com) if you have any questions or suggestions in this area.
There is a Java version of the TFS SDK that will run on Linux, Mac, and Windows. It is the SDK that Teamprise uses.
http://blogs.msdn.com/b/bharry/archive/2011/05/16/announcing-a-java-sdk-for-tfs.aspx
Coding directly against the TFS webservices is not supported (even though people have done it). MSFT could break the interface without letting you know in a service pack or other hotfix. Sometimes there aren't other options, but if the Java SDK works for you, I'd try to use that first.