My son just turned 8, and is in the 2nd grade. He is very small, only weighing 51 pounds. He is extremely healthy and active, but he's tiny. I'm extremely small, too, so he comes by it honestly. ;)
His best friend is large for his age, not overweight - just a big kid. He's very tall, almost my height (4'11") and about 90 pounds.
The boys know they are very different sizes, but they don't care. They mention it from time to time (Oh, those aren't my shoes - they must be yours; they're huge!). At school, my son realizes he's smaller than the other boys, but he doesn't mind. He's outgoing and well-liked. Being small hasn't impacted him negatively at all. As far as your question about when he realized he was small, it was probably the beginning of this year before he realized it (second grade).
An interesting side note - my oldest is 14, and in the second grade he was exactly the same size as my youngest. He was tiny. Now he's in the eighth grade, and he is taller than average, and has a thin, but athletic build. I never would have expected him to be tall, even though my husband is 6'2". He was so small for so long. He just started growing and growing when he was about 12, and he hasn't stopped.
Another thing about having small kids - you mentioned that kids don't take your son seriously. People were always amazed at how intelligent my boys were/are. They are smart (advanced classes, etc.), but much of there perception was because they assumed my boys were younger than they actually were. My boys looked 3 when they were actually 5, so people were amazed at their vocabulary, things like that.
I hope this helps. :)