set: wise specs.. who uses that? life orb if anything giga drain and sludge wave are useless in the set.
partners: scarfty ok.. every thing with a fighting weakness pairs good with gengar as a lure..
EQ and bulldoze(?) the point it? steel types don't scare gengar too much really..
Reflect? gengar can't take a strong pursuit even with reflect.
counters:
metagross- gengar is behind a substitute (cause most gengars are when you switch) metagross used gravity gengar used shadow ball (50%` to metagross)
turn 2- gengar used shadow ball metagross fainted.
Fling iron ball/hard stone first thing who uses it? second sub..
light screen- espeon gets 0HKOed by shadow ball so is latios deoxys-D too and it is counter so they are mostly 2HKoed
Users of- disable says hi.
Trick room- well this kind of helps not a counter though you still need to tank 2 attacks from gengar to beat him.
High Sp. def- blissey and chansey? huh? they can't touch gengar.
zen headbutt bronzong again.. who uses it and it also get disabled.
all the ones you listed after that don't pass disable. Girafarig doesn't resist focus blast and again who the hell uses girafarig in OU?
Ok I used subdisable gengar for 2 days on my team and I must admit it is one of the most useful pokemons ever.. it can just screw Stall and choice users too it is very strong even with timid and leftovers and I can't count the times I managed to set a sub with it and keep it for a while.
I used it with zoroark they work really good they both learn focus miss.
Counters to gengar are actually very few you need to assume it will be behind a substitute to counter it.. taunt is a good way to stop subs but you are still dealing with a pokemon behind a sub. something like cincinno with skill link can counter gengar if you lure it into shadow ball but.. who uses him? nothing resists both fighting and ghost even hipotetical types..
jirachi is neutral to fighting and ghost and have some bulk so it can beat gengar if it have more than 1 attacking move. it is easier to beat gengar if it isn't behind a substitute every scarfer can do that (except scarf magikarp he can't check gengar

) priority scares gengar out scizor can beat gengar when not behind a sub..
To sum up, gengar is only really scary behind a substitute don't let him set up one.. just sacrifice something don't let him set a sub.. it is too damn dangerous.
Oh and gengar's biggest flaw is focus miss not his bad defenses those problems are minor.. focus miss.. if focus blast would be 100% accurate gengar would be THAT annoying it might be uber..