The secure erase feature is still there in El Capitan's Disk Utility.
The trick is to select the volume (not the drive) from the list on the left of Disk Utility.
An erase-this-volume screen appears.
Click the Security Options button in its lower left corner
CleefMon,
Thanks for this post - it was very helpful. Whats odd is that I could swear I looked at this window several times, but since I had already repartitioned the drive I was only selecting the entire drive. The trick is that for some reason Disk Utility doesn't refresh itself anymore. You have to quit and re-open Disk Utility to make the new partition selectable again if you've ejected it. I ejected the partition assuming that I needed to select the whole disk for the secure erase.
This whole conversation about secure wiping SSDs and using FileVault overlooks that many of us still have reasons to physically erase an entire disk. As an IT guy my Mac is my go-to tool when I'm troubleshooting odd problems on other machines (you need something reliable when everything else goes down...). I find myself being the go-to guy for friends and family. So when a neighbor leaves their old laptop with me trusting that I'll take care of cleaning their data, I need the tools to take care of that. So when my erase options have gone missing, I start to wonder what's happening at Apple. No need to worry, everything is the same at Apple. They like to take things you are comfortable with and move them around, so yup everything is the same.
Anyway, there are many many reasons to keep secure erase around. Just now it's per volume instead of per disk. So to erase an entire disk, you have to repartition it to a single volume, then secure erase the new VOLUME, not the disk. And be aware that Disk Utility might not show you the new volume until you relaunch it.