I sincerely apologize for taking so long to get back to you, life has me on the run lately, and my computer time is generally the first sacrificed when time gets short.
I tend, as a rule, to stay away from questions regarding children, as I was not treated (or even diagnosed) as a child, and I have no children of my own. I know, though I can't name the particular effect off the top of my head, that very often, children react differently to meds than adults do, and as such my complete lack of experience is a serious limitation. Case in point, I know that stimulants can have an actual calming effect on children, often leading to complaints of 'feeling like a zombie.' This effect is very different from that experienced by adults, where you often see references to 'a fog being lifted' or 'being truly awake for the first time.' It's clear that while the meds have similar effects in regards to regulating behaviour and increasing focus, the way it makes us feel is entirely different.
That said, all I feel comfortable in doing is quoting my observations from this and other boards. Concerta seems to definitely be the most common med for the treatment of ADHD these days, especially in children. I'm not sure why, but I'm guessing that advertising to doctors is largely responsible. Adderall seems to be the med that most often gets positive reports, but the occurrence of side effects seems to be far more pronounced as well.
As you may or may not know, stimulant based ADHD meds are broken into 2 categories, amphetamine-based meds and methylphenidate-based meds.
Adderall is among the amphetamines, and is made of up four different amphetamine salts. This is why, I suspect, that it's both the most successful and produces the most side effects, unlike other options that are more carefully targeted, Adderall is like treating ADHD with a shotgun, they just throw everything into it and hope one of them works for you.
Concerta is methylphenidate, which is an amphetamine analog, but isn't actually amphetamine. Under the brand name Ritalin, methylphenidate has a very long history of treating ADHD (all the way back to the '50s), and as such has a long track record. That said, Concerta is not straight up methylphenidate like Ritalin is, it's bound with another compound that makes the methylphenidate unavailable until it's been metabolized. This formulation is intended to cut down on the abuse potential of the med, but in my opinion, can limit the bioavailability of the med in people with non-standard metabolisms (either fast or slow). Vyvanse has taken this same approach with amphetamine, and I suspect it will be ineffective for some people for the same reasons.
Unfortunately, the time tested and ultimately most effective method for finding the right drug regimen for ADHD is trial and error. Find a doctor that's willing to experiment and try your son on different meds, always stepping up from the lowest possible dosage to higher dosages, and see how your son responds. If the result isn't what you'd hoped for, or if the side effects are too much, then that med/dose is not the right one. I know this seems like a cop out, but ultimately, we all have slight variations in body chemistry and what works for one may or may not work for another.
In regards to the Clonidine, I truly have no idea. Until recently, the alpha-2 agonists have been exclusively for treatment of tics that often come along with ADHD. The idea that they're useful in countering the side effects of stimulant treatment is somewhat novel, but gaining acceptance rapidly. Another similar medication used for the same purpose as Clonidine is known as Intuniv (or Tenex). This med may or may not work better for your son, I really have no experience with these. The biggest concern with this class of drugs is the risk of low blood pressure, learn the signs of it and keep an eye open.
Other non-stimulant options include Wellbutrin and Strattera. These are reuptake inhibitors (similar to SSRIs that treat depression) that work on the same neurotransmitters affected by the stimulants. I'm having resounding success on Wellbutrin, in conjunction with Adderall, but for the various reasons listed above, your son may not experience the same.
Don't be afraid to contact me with other questions, or if clarification of my ramble here is needed.