They're active on either Google Talk or Google+. Orange means they're idle, red x means they're unavailable.
If they aren't showing a dot, they either do not have an Google account on their phone or they disabled Google+/Talk (my friend, who also owns an S3 did this, and his dot disappeared)
On my Galaxy S4 it will show the green dot now and then for various contacts but the weird thing is they are all iphone users.
If the dot is to signify they are 'online' does it some how get notification from iMessage that they are online?
I bought the phone the day it came out and for a while it never showed this, but for the last 2 weeks or so mainly 3 different contacts will show it.