As of 2005, the only other route with significant sections of jointed rail would be HC, and I believe that to still be the case. Between 21st St. junction and the BNSF (ex-ATSF) crossing at Corwith, (located about a mile south of Brighton Park), both mains are jointed rail, but south of there all the way to Joliet, jointed rail is only present on MT2 (the south main), while MT1 was upgraded to CWR almost ten years ago. And, while both the main line and South Chicago branches of the electric district are totally outfitted with CWR, jointed rail is still present on the Blue Island branch between West Pullman (Halsted St.) and the Blue Island terminal. But other than that, CWR is standard throughout the rest of the system.
I know that the segment between 179th and Manhattan on SWS had been jointed rail until at least 2004, don't know if Metra upgraded that in time for last year's expansion. It has been Metra's stated goal to eventually upgrade the jointed rail segments mentioned above to CWR standards, but if they keep being forced to divert funds from the capital budget (which includes these precise kinds of physical plant upgrades) to the operating budget in order to cover shortfalls, it's a pretty safe bet these areas of jointed rail won't be going away soon...
--Dorian--