When defending a gym, you can not currently affect the battle once your Pokemon is deployed. In contrast to attacking, you have little flexibility, and your goal is no longer to maximise damage, but to minimise it.
Regardless of which Pokemon you choose, there will always be a counter to its weaknesses, your goal is to minimise the opportunities that the attacker has to do high levels of damage.
The need to minimise damage lends itself to a function that scores pokemon highly when they have; few weaknesses, high HP and a high defence score. The above table ranks Pokemon with a score based on these stats.
Pokemon with few weaknesses can be easily identified by their type(s) with reference to the Pokemon Go Type Chart.
HP Can now be calculated with the known formula: HP = (Base Stamina + Stamina IV) * CP Multiplier. We take the CP multiplier for Pokemon at max level 40 and assume the Pokemon to have perfect +15 IVs.
Base defence scores for all Pokemon in Pokemon Go are now known and included in the table above.
HP and Defence score are both the base scores for these Pokemon, before IV's. HP has been calculated for max level Pokemon. This formula we've selected to calculate the final score is:
Score = (Defence + HP)/(Average Weaknesses&Resists * No. of Weaknesses^0.3)
Importantly, this table is ranking Pokemon on their individual ability to defend. It should be used with common sense to craft a diverse team of defenders with your friends. E.g. Chansey might be strong, but using 3 of them to defend a gym leaves it open to destruction by perhaps a single good Hitmonlee.The same could not be said if the gym was defended by a more diverse range of Pokemon from this list.
If you already have a great team of defenders, check out the Attacker Tier List to see the most powerful attackers in the game.
The Pokemon at the top of this list are the same Pokemon people search for thousands of times a day using the Best Attackers or Team Suggest tools. You can see which Pokemon trainers are searching the most at Tips & Misc.
If you like Poke Assistant and the free services it provides, the best thing you can do to give back is to recommend it: