Countering Jirachi is difficult due to the variety of sets is can run.
I usually use a Jirachi that has the following moves: Substitute/Wish/Iron Head/Body Slam. This set can single-handedly defeat a Rocky Helmet Ferrothorn! Leftovers Ferro is a real problem to this set obviously, as a standard ferro takes about 5-10% damage from iron head, effectively PP stalling it.
Red Card carrying pokemon can easily check boosting sets. As mentioned before, Physically defensive Quagsire,Gastrodon are great checks to sub CM Jirachi. Tyranitar can come in on a SubCM Jirachi with Psyshock and can roar it out or hit it with EQ for super-effective damage
Volt-Turn teams (Thundurus-T) can create problems for Jirachi. Scarf Scizor and Thundurus-T do well against any of Jirachi's sets and SubCM sets can played around with.
Fantastic Pokemon, this Jirachi.