If you follow the WCAG guidelines on photosensitivity you'll usually be fine. In a nutshell:
- No more than 3 flashes (Light to Dark to Light transitions) per second. (I'd still squint, but it doesn't hurt)
- Bright red specifically should be avoided.
- There's more leniency if flashing occurs outside the areas of focus (eg in a small corner of the screen).
There's a point about disabling motion entirely, but that's not an option in games outside of screen shake. Additionally I'd try out other means of emphasis depending on the genre and art style. Stuff like:
- Subtle particles
- Squash-and-stretch
- Knockback (for action games)
- Gradual tinting
- Freeze frames
- Dedicated animation frames (if constraints allow it)