When I set up encounters I go through the same basic questions. What's the in-game reason for the encounter? Is it just a logical result of actions by the PCs or others? Does it move the plot forward or add to the story? Will it be fun? Is it logically consistent with the world I envision?
What's the in-game reason for the stampede? What kind of creatures are going to be involved? While people tend to think of forests being where the wild things are, the truth is that prairies or mixed prairie/grassland are where you tend to get large herds, not forests. But it's your world and if it makes sense then go for it.
Next, what's the meta-game purpose of the encounter? Attrition? Flavor text with minimal real danger? A directed stampede as an attack on the PCs? A mix of things with a chance for the PCs to show some ingenuity? As has been mentioned, you can look at expected damage in the DMG, as for the rest I'd kind of play it by ear.
If I were to run a stampede encounter I'd do a lot more than just a single reflex save. Instead of a saving throw what about a reaction/single action? Perhaps a perception to give you advantage to use a skill, if it's high enough to take a full turn instead of just a single action.
After that I'd consider treating it like a combat round with possibility of people being surprised with a swarm/mob trample attack (strength save or knocked prone) with adjustments based on what they attempt.
- Perception 5 or less, the PC is surprised and the swarm "attacks" with advantage.
- Perception 6-10, PC is surprised.
- Perception 11-15, PC has a single action or move half their speed to dive behind a tree or try to grab a low-hanging branch. Nature or investigation check as a reaction to determine where to avoid the herd. Success means they avoid the worst of it getting 3/4 cover and resistance to damage.
- Perception 16+, PC is not surprised at all and gets advantage on the nature or investigation check from above.
- A poor perception (less than 10) means the PC is caught totally off guard and get no bonuses, the "swarm" may even have advantage to hit if the perception check is less than 5.
So basically, if they have a high enough perception check they may avoid the worst of it but then jump behind that fallen tree, it doesn't help that much because it's rotten which they didn't notice when they failed their nature check.
The second (and possibly) third rounds the PCs could help each other, but other thing might happen as well such as trees getting knocked over, etc.
But as I said, it depends on what the purpose of the encounter is. It could just be as simple as box text that you narrate for flavor or have other complex situations as a result of the stampede. It also kind of depends on what is stampeding - a colony of rabbits running by is odd, a herd of elephants could be deadly and knock over trees.