My dd1 was in the 3-5% for weight (or off the charts) and in the 90-100+% for height until she was four. I think she's up to the 20% now for weight.

She was allergic to egg at the age of two (and avoiding peanuts/treenuts/fish/shellfish, had JUST outgrown her dairy allergy at that age).
We worried a lot about her weight and I did a lot to try to get more calories into her food. Fortunately she didn't do too many of the toddler 'living on air and water' episodes, she had a big appetite and held off 'til she was three for the periods where she didn't really eat much of anything.
It was at her two year appointment when my dh commented to the Ped, "You know, I think I was in high school before I was ever above the 10th percentile for weight." And we know that I was a skinny kid too. So genetics were likely partially in play at least with her. Having watched dd2 (also with allergies, but ones identified before near-FTT, which is how we really got dd1's under control) - she was a CHUB as a babe but has slimmed down to not too different a build than her older sister at the same age. So I suspect that part of Ina's skinniness was because she never laid on that early baby fat that her younger sister was able to lay on. It's just a theory though.

I didn't read
Child of Mine until this past summer, and I wish I'd read it when we were worrying so about dd1's weight. It's written by an RD about childhood nutrition and is backed by a lot of different research studies about infant and child nutrition. I think if I'd read it, I would have worried less about dd1's weight, and at the same time, I would have known more about how to discuss/move forward with her allergy and food issues. I really recommend that you read it!!
That said -
A. Are you certain you are aware of all your little one's allergies? Ina plateaued on her weight gain for the three months that I was eating eggs occasionally. She showed no other sign of an allergy other than the halted weight gain (9-12 months). Once we directly introduced eggs to her, we realized what had been happening.
B. I know there are lots of reasons to wean, and I don't want to pressure you. But have you considered letting your little one continue to nurse for another six months or so, to see if his appetite and weight gain catch up? Ina nursed 'til she was 2 1/2 and I think it made a difference for her. Right now, you have a low-weight kiddo and it's one of his favorite foods. Removing that food from his diet doesn't mean he's going to eat other foods to make up the difference. I know this is frustrating and it's often the first assumption that people make to 'solve it.' But your milk is a high-calorie food and it's got antibodies etc. to help keep him healthier while he's low weight.
Look for
Child of Mine at the library - you can skip the infant feeding sections and go directly to the toddler stuff (you might need to skim a bit of the intro and infant sections) and then apply it.
