Deoxys-D takes hits like NOTHING and Recovers right in your face with Pressure.
Deoxys-D is the best Spiker in the game, hands down. It survives both physical and special hits, cannot be trapped by Magneton, and gives Dugtrio a run for his money. This is the standard Deoxys-D set.
Deoxys-D has 216 Speed without any EVs, which is plenty for Agility to work out fine. The premise behind this is that the most common counter to Deoxys-D is a Pokémon that makes 101 HP Substitutes, and most everything is faster than Deoxys-D. Lots of times, it's possible to Toxic one enemy, say Rayquaza, but then if they switch out to something that makes 101 HP Substitutes, it's easy to catch you unaware, so you can't Toxic them on the switch. Another common occurrence is that after one enemy dies to Toxic, they'll send out a substituting Pokémon or a Taunting Mewtwo, preventing you from doing anything useful. If you first Toxic whatever's out there, then Agility, problem is solved. You're too fast to be Taunted, and if the enemy tries to hide behind a Substitute, you get in a Toxic first, so the Substitute only quickens their death. Many people don't even realize you have Agility, even once you use it, so they are extremely surprised when you kill their Rayquaza and Kyogre.
This also allows you to do stuff like Knock Off Deoxys-A's Choice Band before it can use Shadow Ball (and Knock Off does over 30% to Deoxys-A).
Taunt stops Blissey from ruining your fun with Aromatherapy, and shuts down stallers like Toxic Lugia, Blissey, and other Deoxys-D. If Blissey tries to pull a fast one on you and use Icy Wind to cut you down to size, just use Agility again every once in a while, and the problem is solved.
A stalling, defensive set. Doesn't work nearly as well as others, especially not with the prevalence of Whirlwind Lugia + Aromatherapy Blissey.
Rest is preferred over Recover to heal Toxic.
Deoxys-D actually makes a decent Calm Minder, because it can take physical hits after setting up. You can either go for an option to damage Darks and Steels, or take the option of Taunting all recovery / status from Blissey, as well as pseudo-hazing (primarily Lugia). Either works. Use Recover with Taunt, Rest with the elementals. Psychic and Ice Beam both work as your only attack, but always use Ice Beam with Thunder or Thunderbolt. Toxic is your only hope at beating other Calm Minders, honestly. Save the surprise of Toxic if your opponent has Safeguard Latias or Latios, because when they see Calm Mind, they probably won't expect it.
Taunt is used to force the enemy to attack, and then you Counter and Mirror Coat accordingly, while Recovering off damage. This only works with Spikes, otherwise, they can just keep switching around.
Snatch is awesome for stopping 101 HP Substituters. It also works well for catching Kyogre Calm Minds and tanking even better. Torment makes life hell for a whole lot of sweepers.
Superpower helps against Blissey, since a lot of them think they can stay in and Toxic you, and run little to no defense in Ubers; it also does a lot to Tyranitar. Ice Beam makes it counter Rayquaza even better. ExtremeSpeed makes it a poor man's counter to Ninjask, Flailers, and Deoxys-A (the Substitute / Petaya version in particular). Thunder is a decent option on the Calm Mind set to hit harder in rain.
Reflect and Light Screen are always good moves on a tank like Deoxys-D.
Max HP always. Taunting versions without Agility will need a little bit of Speed to be faster than enemy Deoxys-D. Otherwise, just pump those Defenses.
Checks and Counters
Blissey can Toxic you if you don't Taunt, Rest, or Aromatherapy, which puts an end to Deoxys-D. 101 Substitute Pokémon like Kyogre and Groudon work if you can avoid a Toxic. However, if Deoxys-D sets down Spikes, you just make it run, possibly to Lugia, who will Whirlwind most counters away for Spikes damage. Taunt Mewtwo really gives it trouble. Latias and Latios with Safeguard or Refresh beat it 1v1, but the threat of Knock Off keeps them at bay. Choice Band Metagross 2HKOs with Meteor Mash. Swellow and Heracross love that Toxic, and Heracross just destroys it regardless, same for Scizor.