Currently there is no interface exposed for this. You can do it via JavaScript, but be aware that this is an unsupported access and may break in the future.
This JS adds a link to the right of the "Wiki" menu item at the top:
$(document).ready(function() { $('#Menu_Wiki').after('<span><a class="navlink" href="default.asp?pg=pgPlugin&sPluginId=plugin@example.com">My Plugin</a></span>') });
This JS adds a link to the left of the "Working On" menu item at the top right:
$(document).ready(function() { $('#belowBanner').prepend('<span><a class="navlink" href="default.asp?pg=pgPlugin&sPluginId=plugin@example.com">My Plugin</a></span>') });
This JS adds a link to the right of the "Help" link at the top right:
$(document).ready(function() { $('#Menu_Help').after(' | <span><a class="navlink" href="default.asp?pg=pgPlugin&sPluginId=plugin@example.com"><span class="dotted">My Plugin</span></a></span>') });
Edit
Remember that this is an unsupported access, and Fog Creek makes no guarantees about its support in future versions. We will not, however, ban plugins from the Plugin Gallery or FogBugz On Demand for using this method to add a link to the top menu.
We do plan to add a supported interface for this in a future version.
Addendum
To make the script run on every page in FogBugz, use an interface like IPluginStaticJS to add a static JS file that is included on every page.