I have a couple of things to say.
First, while the Pacific Surfliner runs in the median of the 5, it is for barely more than a mile south of Stuart Mesa (that is the name of the yard where Metrolink and Coaster store many of their trains). The rest of it has an arrow straight line and can get really fast. I think the speed limit may be 90, but I'm not sure. Back when I was six, my grandma (the same one I go to visit) used 10-rides and came down every Friday afternoon and left every Sunday evening. Sometimes, she would come down a day early and take us back up with her to spend the weekend in LA. She got to know many of the conductors very well, and one specifically named Franklin, who hasn't worked for Amtrak in a while, once brought all four of us (me, brother, sister, grandma) into the cab car just to show us what it was like. He knew how much I was into trains, even at that age, and we met the engineer. It was one of the coolest experiences. We were travelling south through Pendleton, before the 5 crosses to the west side of the tracks. The engineer let us honk the horn, and I remember seeing the speed gauge hit 93 at one point (don't worry, I promise he didn't let us control the train
) Right before we left, a crow smacked the window that the engineer sees through.
On the Pasadena tracks, they were torn up in the early 90's. They were restored as part of the fully-double-tracked Gold Line in the early 2000's to Sierra Madre (really in Pasadena, not yet Sierra Madre, but names after the street). They are currently working on extending the Gold Line to Azusa further down the San Gabriel Valley, with all of the new track staying in the median of the 210. This will be hard, since the previous right of way does not extend that far, but wen I was on the 210 a few months ago, I saw crews at work already grading.
Here is a link to the exact spot where the tracks used to exit from the 210, basically right next to Santa Anita:
http://maps.google.com/?ll=34.148008,-118.038939&spn=0.00356,0.005284&t=h&z=18
For Swadian, here is a pic of the tunnel the trains enter to get into the median of the freeway in downtown Pasadena:
This is the old train station that the Southwest Chief stopped at before going via Fullerton:
Last, here is the Gold Line running through the median of the 210 as it does today. Notice the VERY LIGHT (yes, VERY LIGHT, honestly no sarcasm involved, it's a sucky freeway) traffic:
Cirdan was right that at least one station is in the median of the 25 on the Rail Runner system. It is the Cerrillos Rd. station on the very south side of Santa Fe, the first station after the tracks split from the historical Glorieta/Raton Pass route.