Windows 8 added deprecated old-style file registrations. An application must register a ProgID and Capabilities in order to advertise a URL handler in Windows 8 and above.
Jason Harmer has a helpful blog article pointing out the specific key needed for Lync, and we can translate and add the missing entries to get it working for Jabber. Save the below to a .reg file, and Jabber will appear in the menu.
Windows Registry Editor Version 5.00
[HKEY_LOCAL_MACHINE\SOFTWARE\WOW6432Node\Cisco\Jabber (ITP)]
[HKEY_LOCAL_MACHINE\SOFTWARE\WOW6432Node\Cisco\Jabber (ITP)\Capabilities]
"TEL"="callto"
[HKEY_LOCAL_MACHINE\SOFTWARE\WOW6432Node\Cisco\Jabber (ITP)\Capabilities\UrlAssociations]
"tel"="Cisco.Jabber.ITP.telhandler"
[HKEY_LOCAL_MACHINE\SOFTWARE\WOW6432Node\RegisteredApplications]
"Cisco.Jabber.ITP"="SOFTWARE\\WOW6432Node\\Cisco\\Jabber (ITP)\\Capabilities"
[HKEY_LOCAL_MACHINE\SOFTWARE\Classes\Cisco.Jabber.ITP]
[HKEY_LOCAL_MACHINE\SOFTWARE\Classes\Cisco.Jabber.ITP\CLSID]
@="{46B1B0A9-6C89-476A-BD0E-4A83EBC8D644}"
[HKEY_LOCAL_MACHINE\SOFTWARE\Classes\Cisco.Jabber.ITP.telhandler]
@="URL:Cisco Jabber Protocol"
"URL Protocol"=""
[HKEY_LOCAL_MACHINE\SOFTWARE\Classes\Cisco.Jabber.ITP.telhandler\DefaultIcon]
@="C:\\Program Files (x86)\\Cisco Systems\\Cisco Jabber\\CiscoJabber.exe"
[HKEY_LOCAL_MACHINE\SOFTWARE\Classes\Cisco.Jabber.ITP.telhandler\shell]
[HKEY_LOCAL_MACHINE\SOFTWARE\Classes\Cisco.Jabber.ITP.telhandler\shell\open]
[HKEY_LOCAL_MACHINE\SOFTWARE\Classes\Cisco.Jabber.ITP.telhandler\shell\open\command]
@="\"C:\\Program Files (x86)\\Cisco Systems\\Cisco Jabber\\CiscoJabber.exe\" -URI %1"

Edit: Cisco Jabber does have problems parsing the tel: uri, so it may be helpful to run it through another script before calling jabber. An example is posted on Gist and can be compiled with csc Program.cs. Prepend the full path of the compiled executable to the default value of the HKEY_LOCAL_MACHINE\SOFTWARE\Classes\Cisco.Jabber.ITP.telhandler\shell\open\command key.