Error when updating eclipse

What version of eclipse are you using ?

It has been fixed in 3.4.1, but in your case, it could be this bug instead.

It turns out the cause is one or more artifact repositories being lost from the list of known repositories.

The workaround is to remove the repository from the list and add it back again. This restores the missing artifact repository.

A possible workaround in eclipse 3.4.1:

1. export the update site listing to bookmarks.xml file (Software Updates->Manage sites->Export)
2. stop eclipse
3. remove configuration/.settings/org.eclipse.equinox.p2.*.prefs files
   (Note, as mentioned by Fredrik in the comments, for Eclipse3.5+, this would be:
   p2\org.eclipse.equinox.p2.engine\.settings
p2\org.eclipse.equinox.p2.engine\profileRegistry\SDKProfile.profile\.data\.setti‌​ngs)
4. start eclipse
5. import the bookmarks.xml file (Software Updates->Manage sites->Import) that was exported in step 1

As mentioned by mark (author of this question) in the comments of this answer, that workaround was a solution for his problem.

Other advice:

[…] the solution is always to append a trailing "https://stackoverflow.com/" to all repository URLs in my P2 UI.
My feeling is that this error is caused by a failure to construct a viable URL to a repo resource. The code in question is not inspecting the URL string from the UI and is assuming a trailing “https://stackoverflow.com/” resulting in a 404

This last solution is confirmed working in Eclipse Indigo and Juno (below in the comments).