Collision groups, so we can set group of object and groups that this object will collide it (for others it will simply phase through). Even simplest solution like in Algodoo (where you have fixed number of groups marked with big letters) would be good.
Per-object gravity setting, so we would have smaller gravity for one object, but bigger for another.
There will be more suggestions, but I gtg.
You can modify the weight of the object to make it more or less reactive to the gravity.
Yeah, but it’ll be also more or less reactive to forces applied to object, when sometimes we just want different downward force (gravity). Also weight/mass of object doesn’t affect speed of falling of it. Damping a.k.a air-resistance does.
You can simulate a different gravity by simply always adding a small force to some objects.
I know that, but it’s tricky and hackish. I’m talking about clean solution.
How about my first suggestion (collision groups), though?
That’s a clean solution, especially when you consider using objects groups.
You just have to create for example two or three objects groups ( Name them “HighGravityObjects”, “LowGravityObjects” for example ) and then to add a single event with two actions to add a specific force to these two objects groups.
Advantages :
-As you’ve created objects groups, you can very easily see which objects are affected by a specific gravity, and you can easily add an object to a group.
-You are sure that every object in a group have the same gravity : You cannot make a mistake by setting a different gravity to an object which should have the same gravity as another.
-You can change the gravity applied to a whole object group by changing a single number in the events : No need to edit each object automatism.
Moreover, others users of the physics automatism maybe don’t need a “per object gravity”, and I think that it’s better to try to avoid unnecessary features : I don’t want to have to maintain an oversized software bloated with functions that can be very easily recreated with a single event. 
Collision groups would be a good idea