The year I did it, I got an e-mail after I registered saying my application would be accepted once they varified my qualifying time. About two or three weeks later, I got a second e-mail saying I was in.

From talking to those that do the race regularly, if you qualify and apply by the deadline, you should get in to that year's race. Have you not heard from the BAA yet? How long ago did you apply?

First-time qualifier for 2006 here. September is when they accept applications for the following year.
It is a very easy process. Most marathons automatically forward their
results to Boston. In general, if you qualify in a marathon AFTER (but
not including) the last weekend in
September, you are eligible for the
next TWO years in Boston. If you qualify in a race prior to, and including the last weekend in September, you are eligible for only
the following year. Entries are accepted first-come, first-serve, up
to around 20,000, and generally does
not fill up until late Jan or Feb.
Entry fee is around $100, and is non-refundable and non-transferrable. If
you get injured after qualifying, as I
have unfortunately done, you have until April 15, 2006, to request a
medical exemption for the following year and your qualifying time will still be honored. In 2006, for the first time, runners will be divided
into two waves. The first wave (under
3:30) will start at noon, the second
wave (over 3:30) will start at 12:30.
You will still be in corrals according
to your time within each wave. You can move to the back of a corral, but
not up, and you cannot change waves.
I was told I could walk the route (I've got IT band syndrome and can
barely run a mile at present) but if you don't finish in 6 hours, you will not be a part of the official and you
are not guaranteed a medal. A limited number of spots are also available for non-qualifying runners who are willing to raise funds for Children's Hospital. Have I left anything out? Probably, but GOOD LUCK!