Rules to gyms of course vary greatly however here are some rules ALL Johto gyms must oblige by(Most rules repeat that of kanto):
1. You may have no more than THREE challenges for your gym courses.
2. You may not limit weapon type, only material type. eg You may use no greater than stone weapons (allowing anything from a block, wood weapon, stone weapon, or a bow.) or iron weapons (everything listed previously + iron weapons (sword, axe) and unarmed.
3. If you log off DURING a challenge you do owe the challenger $500. this means if you leave with a challenger actually in the course, not someone saying "hey i challenge you"
4. You may allow a wait time to having someone re-challenging up to a max of 3 hours. The time has to be set, you cant make someone you dont like wait while allowing others to rechallenge directly after or with a shortened wait time. favoritism isn't cool.
5.If your gyms allow wolves, you may not have more than 5 wolves for your fight.
6. You ARE allowed to limit other things, such as items (enderpearls, food, potions ect.) and enchants(this means allowing or disallowing enchants, not specific enchant types, furhtermore you can say enchanted armor only, or enchant weapon only, but not enchant swords only ect.).
7.If the gym fight results in a tie, the challenger recieves the badge. Ties are impossible with death messages.
8. if the challenger dies, course or battle, you must return ALL of his items. (items falling in fire or lava of course cancels out this rule) Arrows Included
9. As a gymleader if you have any problems with your course or arena and want to remodel you must first have held the position for more than 1 week and than recieve admin approval for a remodel.
10. as a gymleader if you choose a co leader, you do not become the boss of him, you are each partners and cannot "fire" him if you decide you do not like him.
11.You cannot recieve payments for anything in your gym. example : nerfs of course, accepting challenges, selling badge. ect.
12. you cannot give out your badge to anyone who has not beaten you and your course.
13. If you are a gymleader and wish to get your own badge, you must challenge your co-leader, and do your own course prior to the fight, if you do not have a co-leader you may ask an admin to fill in as a gymleader for your challenge.
14. No Parkour
Im sure there are some things ive forgotten and i will edit later as i remember. anything anyone would like to add just tell me and ill edit it in.