What to use:
Nature: Timid
EVs: 252 HP / 4 SpA / 252 Spe
Item: Leftovers
Moves:
- Substitute
- Calm Mind
- Thunderbolt / Thunder
- Psyshock / Flash Cannon / Water Pulse
Role: Special Sweeper, Stallbreaker
What it does: Jirachi is a great sweeper, and even a pseudo-mixed sweeper if you choose Psyshock as the last move. It is one of the few special sweepers that laugh at Blissey/Chansey, as it can use Substitutes that will not be broken by Seismic Toss, and can use them as setup bait. Calm Mind slowy strengthens Jirachi, and also boosts its Special Defense, which means that if your opponent doesn't have a super-effective physical attack against this thing, Jirachi can potentially boost to the point that it will be unstoppable.
Calm Mind is there for obvious reasons. Substitute protects Jirachi from status, and facilitates prediction. For example, if your opponent brings something like Infernape (not that someone experienced would use him), and Jirachi uses Substitute as it switches-in, Infernape will be OHKOed by Psyshock.
An Electric-type attack is necessary to achieve the best neutral coverage possible with the last move. Thunderbolt is the primary option, but on a rain team, Thunder can replace it, as it is not only stronger, but thanks to Serene Grace, has a rage-inducer 60% chance of paralyzing your opponent.
The last move comes down to preference. Psyshock is the recommended option, as it has great coverage with Thunderbolt, and maims the common Fighting-types, such as Terrakion on the sand. Psyshock also lets Jirachi easily bypass the pink blobs after two or three CM boosts. With Psyshock, Jirachi is somewhat of a mixed sweeper, as it can hit specially defensive Pokémon with it, and physically defensive Pokémon with Thunderbolt. Flash Cannon is another great option. It lets Jirachi bypass Celebi, Tyranitar and physically defensive Ground-types like Gliscor, because the former two are resistant and immune, respectively, to Psyshock, and take little damage from Thunderbolt, and the latter doesn't take much from Psyshock because of their enormous physical defense.
However, on a rain team, Water Pulse is another great option. It is weak and doesn't have that much neutral coverage with Thunder (in fact, it misses out Dragon-, and Grass-types) but it has a 40% chance to inflict confusion status. Thogeter with Thunder's 60% chance of paralysis, your opponent will actually have a hard time trying to defeat Jirachi, and will be defeated one time or another with repeated Thunder/Water Pulse and confusion damage. If this doesn't happen, at least your opponent will be crippled by paralysis.
Good Teammates: Anything that has resitances and/or immunities to Ground AND Fire is a good partner. This includes: Dragon-types like Lati@s, Salamence, Dragonite, Hydreigon, as well as Balloon Heatran, and Gyarados. They are generally capable of switching-in on Jirachi's weakness, and then wrecking avoc by defeating whatever Jirachi has problems taking down. As you may noted, Jirachi has serious problems against many Ground-types. For this reason, Grass-types are amazing partners, especially Ferrothorn and Celebi. The former has hazards that facilitate Jirachi's work, and the latter can defeat almost any Ground-type, and can even check dangerous Pokémon for Jirachi, such as Sheer Force Landorus. Politoed is another amazing partner. Politoed checks most Ground-types, and summons a rain that negates Jirachi's weakness to Fire. Not to mention that Jirachi is able to use Water Pulse + Thunder to hax the opponent.
What Counters it: As was mentioned numerous times above, Ground-types are good counters for Jirachi, most of time, especially if they are physically defensive. Hippowdon and Gliscor deserve mentions, as they laugh at most atempts of Jirachi to do anything. The former can even phaze Jirachi if she dares boosting even more. Even if Jirachi carries Water Pulse, it is better off switching-out. Dugtrio traps and kill Jirachi before it can do anything. Jirachi's only chance is if Dugtrio do NOT carry Focus Sash (or if Stealth Rock is on field) and Jirachi has 1 CM Boost, an intact Substitute and Psyshock (or Water Pulse on rain). This way, as Dugtrio breaks Jirachi's substitute, it is OHKOed by Psyshock (or Water Pulse on rain). However, this is a very obscure situation that is unlikely to happen most of time, so Dugtrio remains a serious threat to Jirachi. However, the worst of them all is Quagsire, as it ignores all Jirachi's boosts.
Apart from Ground-types, Jirachi has problems with Fire-types, although they are less effective than Ground-types in terms of taking down Jirachi, for three reasons. The first is that all of them are weak to Stealth Rock, with exception of Heatran and Infernape (I am only speaking of common Fire-types). The second is that most of them aren't immune or resistant to Electric, so Jirachi can simply hit them with Thunder(bolt) and then switch-out as they break its Substitute. The third is that Jirachi's Fire-type weakness can be negated by rain, and in fact, on rain, expect Jirachi to carry Water Pulse, a move to which Fire-types are weak.
Ferrothorn resists all attacking moves that Jirachi can possibly use, but if Jirachi has an intact Substitute, Ferrothorn can't annoy him with Leech Seed, and Ferrothorn risks being haxed by Water Pulse + Thunder variants. The same applies to Magnezone, which although can trap Jirachi, actually has problems taking her down as Jirachi can boost her Special Defense to the point that Magnezone can't effectively trap her.
Tyranitar is an annoyance to variants with Psyshock, as Jirachi has to boost various times to OHKO with Thunderbolt, and Tyranitar can easily break Jirachi's substitutes with Crunch. Specially Defensive Celebi resists all moves that Jirachi uses, apart from Flash Cannon, and can use Perish Song to force her out. The same applies to Latias, that can phaze Jirachi. It can even CM alongside Jirachi, but unless it packs phazing, Jirachi will almost always win the CM war due to her double resistance to Psyshock and the fact that she almost always carry Psyshock herself.
Any Additional Info: Jirachi is an amazing Pokémon for teams that want an versatile special sweeper that can even take down the uncommon stall teams. The good of using Jirachi is that it doesn't actually require Rapid Spin support, as it is immune to Toxic Spikes and resistant to Stealth Rock. Actually, Jirachi is one of the special sweepers that require the less support possible. Jirachi is an special sweeper that inspires a fear on the trainer's hearts, that as Jirachi slowy boosts, it become more and more impossible to take down. Expect teams without Earthquake to lose to Jirachi if they don't have another way to defeat her.