There was a little Strong Bad skit about Ruffle posted to @StrongBadActual twitter... gives me hope that Homestar Runner's content will be preserved as is.
The Brothers Chaps will probably end up switching from Flash to Ruffle on their own site eventually, but until then, the Internet Archive has almost all the Strong Bad Emails archived here playable with Ruffle.
https://archive.org/details/softwarelibrary_flash_strongbad