The first set on the Dusknoir analysis (Careful, 252 Hp, 180 Sd) vs. the first set on the Deoxys-S analysis, using Shadow Ball: 49.66% - 58.50% The Deoxys-E set might be taken "out of context", since it was meant for ubers, but I'm sure that it'll keep it's special attacking orientation in standard, because it's movepool is largely special. So, Dusknoir isn't really a counter. It has Shadow Sneak, yes, but if Deoxys switches out on it, you're out of your Deoxys-S counter, since it definitely can't switch in again and hope to live.
Standard Careful Spiritomb vs. the same Deoxys-S, this time using Ice Beam: 35.20% - 41.45% So Spiritomb does take less than Dusknoir, but this is still a 3HKO on a Pokemon without a reliable recovery move (and lower Hp). It does force Deoxys to make a tough decision (between getting Sucker Punched, or getting Pursuited). But Sucker/pursuit only have a very small chance of OHKO: 86.31% - 101.66%. That's with 144 attack EVs. Shadow Sneak isn't a good option for countering it, since it's power is half of Sucker Punch's power.
39.87% - 46.98%- That's the same Deoxys-S set using Grass Knot vs. Vaporeon, one of zxn666's recommended "bulky water" counters. This is assuming that Grass Knot is at 60 base power vs. Vaporeon, I forget what it is. :[ Vaporeon has Wish, but no "instant" recovery move (unless it wants to give up one of it's many useful options for Protect, which Deoxys-S can predict the second time 'round and switch out on), so this is sufficient to say that Vaporeon is not an awesome counter.
62.72% - 73.71%- A Deoxys with Tbolt > Grass Knot vs. the same Vaporeon.
54.36% - 63.90% - That's Vaporeon's best effort (Surf, with 68 Sa EVs) against Deoxys-S.
Damage calcs vs. Swampert (another bulky water "counter") would be a joke, it OHKOs even without an item. However, Here's standard Swampert vs. Deoxys-S.
Hydro Pump, 56 Sa EVs: 55.19% - 65.15%
Earthquake: 53.53% - 63.07%
So it's defenses aren't that bad. It's not like tanks are switching in and getting OHKOs, and it's not one of those, "Add SR, Spikes, and Sandstream damage" cases, DeoS can survie those, too, even coupled with attacks. These are not DeoA's paper defenses, they're similar to Azelf's (Azelf's defenses aren't great, but not too bad...).
So I did "bulky ghosts", and two "bulky waters". I'll do more if you want, this discussion needs some calcs.
It is limited with only four moveslots, but there's the risk it'll carry the move, so you can't switch your Dusknoir into DeoS with too much confidence, without testing a lot (making that "counter" Poke not as much of a counter any more). So, Blissey might counter some sets, but she can't be too careful, or Calm, since she needs her Def against this guy. :P Even when you're prepared, countering it would be pretty risky business.