From EAA news letter
Big Win for Experimental Aircrafton AD Applicability

EAA and experimental category aircraft owners waited a long time for this piece of good news, but it finally arrived on March 12, when the FAA published an updated Advisory Circular (AC 39-7D) on Airworthiness Directives (ADs). The circular formally set FAA policy that ADs are not applicable on non-type certificated aircraft, except when specifically noted. This is an issue that has been on EAA's "Top 10" list of advocacy issues and has been part of the agenda at the last three EAA/FAA Recreational Aviation Summits. The absence of FAA headquarters guidance had created a patchwork of regional policies that varied and at times conflicted with each other.

More here.
http://www.eaa.org/news/2012/2012-03-15_win.asp

Seems like an experimental aircraft with a type-certified engine would not be exempt from AD's issued against that engine, if the engine is to remain type-certified. I don't know if this is much of an issue except maybe when flying off the test-flight hours-- I understand that's a 20-hour required when the engine is type-certified, as opposed to 40 hours for experimental. Eh?
I do think it's a good idea to at least give it some hard thought when an AD comes out on anything on your airplane. For example, there's an AD on the Avcon mufflers used on Avcon C150/150 engine conversions, for cracking where the tailpipe welds onto the muffler can. The AD is technically not applicable to my muffler due to s/n, but guess what? It cracked right where the AD talked about. I'd been watching it so it wasn't a big surprise when it happened, and I had the muffler can rebuilt with heavier material so it woldn't happen again.

As long as it remains experimental then it remains exempt. If you want to individually keep your engine as type certified that would be up to you, not the FAA. What is wise, is another question. I would absolutely check and comply with any AD that I thought affected the safe operation of my plane. I just am not required to so by the FAA, unless "specifically noted" to apply to the experimentals. If I choose not to comply with the other AD's, then operating like that becomes part of my "experiment."

So far, on my own experimental I have watched the Superior Air Parts website and checked my engine against serial numbers that have shown up. One time my serial number missed out on Slick Mag recommendation and another was the new float recommendation by Precision, so far my numbers have not come up. I did have a prop strike and I followed all engine shop recommendations from Superior for tear down and inspection the same as if it had been a certified engine. I will add that the insurance picked this expense up the same as if it had been certified. I wonder if this ruling could change some of that where an AD is put out for a particular certified engine but the owner does not comply because it is installed in an experimental and is not required. Does the insurance company defend his loss the same now? Lowflyby maybe will do us a new video on this one.