Tinker infinite sheep, Bane refresher ult turn away from her, Storm with sheep pull when she ults and sheep in the same circumstance, or just nuke her down with at least 2 good tanks. Orge Aghs, Orchid Halberd.

brewmaster is the NUMBER 1 counter to her.

Outside of hero picks, blink boots and a heart are very helpful against her. Just blink away when she starts the stone gaze and heal up. MKB negates her evasion as well. Just have a lot of damage and you should be fine to kite her around. Silver edge is also a great item in general, since it decreases the damage bosses deal, and you can just go invis when the stone gaze starts.
As for hero picks, the standard percentage damage dealers like doom and enigma do the job easily. Heroes with a permanent stun/silence also work pretty well. Some other interesting heroes are:
Slark: His ultimate with silveredge makes him almost unable to be killed. Also his purge removes the stone effect, and you can have dark pact going almost constantly I think.
Oracle: His ultimate goes purges through Stone gaze, and he has the ability to disarm medusa almost permanently.
Abaddon: Incredibly tanky, ult purges stone, and makes him almost unable to be killed ever.
Ursa: Stacking damage with lifesteal. Just imagine that all the late game bosses are just versions of roshan. Also his ultimate makes him very difficult to kill if activated at the right time.
Shadow Demon: His illusions last a long time, being almost permanent I think with octarine core, and deal insane damage. That and he has a major damage increase. Makes a lot of boss fights much easier.
Alchemist: He's just insane in this mode.
Slardar: Very high armor shred on his ultimate, and also he has a bash with no cooldown, which combined with the very high attack speed you easily achieve in this game, and MKB's minibash, you can essentially permastun a boss while dealing severe damage.
Lifestealer: Against boss enemies, his feast heals him for like several hundred health an attack, so he never dies. Also deals in percentage damage, of course this is current health and physical, so it is the weakest of the percentage damage dealers, but he just heals so much he is amazing against bosses like Medusa. Also has an additional healing spell in open wounds if you really need the healing.
Sniper: He can engage her outside of her attack range, and sometimes outside of her stone gaze proc range. That and the fact that he will be dealing almost permanent headshot slows means that Medusa isn't going to be able to attack you or chase you very easily.
Sven: Dude deals insane damage with rapier, plus has has a lot of bonus armor and a stun, so he is usually good for this.
Pugna: Haven't tried him myself, but apparently you can just decrepify yourself either permanently or almost permanently, so you don't take any damage from medusa. I think this also works for most of the other late game bosses, but don't try it against the year beast, as that may result in instant death due to RP.
Heroes with a form of evasion like PA, Brewmaster, and Windranger are good against her, but except for the year beast, most of the bosses after Medusa have true strike. Void is a good compromise due to it being damage evasion rather than attack evasion. Also heroes with critical strike such as Wraith king, PA, and juggernaut do well also just due to having much higher damage output than most heroes.

for hardcore carries, i suggest satanic so you can tank her atk, mkb because she has a butterfly. also when she got her ulti just try to disable her somehow before you frozen. if your hero doesnt have any kind of disable, abyssal blade may help.

Originally posted by High Octane Wildebeest:

Outside of hero picks, blink boots and a heart are very helpful against her. Just blink away when she starts the stone gaze and heal up. MKB negates her evasion as well. Just have a lot of damage and you should be fine to kite her around. Silver edge is also a great item in general, since it decreases the damage bosses deal, and you can just go invis when the stone gaze starts.
As for hero picks, the standard percentage damage dealers like doom and enigma do the job easily. Heroes with a permanent stun/silence also work pretty well. Some other interesting heroes are:
Slark: His ultimate with silveredge makes him almost unable to be killed. Also his purge removes the stone effect, and you can have dark pact going almost constantly I think.
Oracle: His ultimate goes purges through Stone gaze, and he has the ability to disarm medusa almost permanently.
Abaddon: Incredibly tanky, ult purges stone, and makes him almost unable to be killed ever.
Ursa: Stacking damage with lifesteal. Just imagine that all the late game bosses are just versions of roshan. Also his ultimate makes him very difficult to kill if activated at the right time.
Shadow Demon: His illusions last a long time, being almost permanent I think with octarine core, and deal insane damage. That and he has a major damage increase. Makes a lot of boss fights much easier.
Alchemist: He's just insane in this mode.
Slardar: Very high armor shred on his ultimate, and also he has a bash with no cooldown, which combined with the very high attack speed you easily achieve in this game, and MKB's minibash, you can essentially permastun a boss while dealing severe damage.
Lifestealer: Against boss enemies, his feast heals him for like several hundred health an attack, so he never dies. Also deals in percentage damage, of course this is current health and physical, so it is the weakest of the percentage damage dealers, but he just heals so much he is amazing against bosses like Medusa. Also has an additional healing spell in open wounds if you really need the healing.
Sniper: He can engage her outside of her attack range, and sometimes outside of her stone gaze proc range. That and the fact that he will be dealing almost permanent headshot slows means that Medusa isn't going to be able to attack you or chase you very easily.
Sven: Dude deals insane damage with rapier, plus has has a lot of bonus armor and a stun, so he is usually good for this.
Pugna: Haven't tried him myself, but apparently you can just decrepify yourself either permanently or almost permanently, so you don't take any damage from medusa. I think this also works for most of the other late game bosses, but don't try it against the year beast, as that may result in instant death due to RP.
Heroes with a form of evasion like PA, Brewmaster, and Windranger are good against her, but except for the year beast, most of the bosses after Medusa have true strike. Void is a good compromise due to it being damage evasion rather than attack evasion. Also heroes with critical strike such as Wraith king, PA, and juggernaut do well also just due to having much higher damage output than most heroes.

The one thing I wouldn't agree with is Shadow Demon, since you can't target creep heroes with Disruption. Still, i've tried all your other suggestions and they were amazing, especially Sniper. Thanks : >

You target yourself with disruption. Get items like hallowtide rapier and things which increase base attack damage such as octarine core and blink boots (both give a healthy amount of intelligence), then the illusions are dealing a percentage of your base damage (which can be around 500-600). Each illusion deals 90% damage last I checked, so that is about 180% of your base damage being dealt. Only problem is that they don't get attack speed buffs or the stat gains from tomes, so it isn't exactly 180% of your damage being dealt, but they are still very tanky and damaging for illusions. And then with soul catcher that is a major damage amplification, so he can potentially deal a ton of damage to solo targets.
Some other heroes which can be good are:
Vengeful spirit: very high agility gain, as well as her damage aura being insane in this mode due to items such as hallowtide rapier giving base damage. She also has a decent stun and good amount of armor reduction, so she can deal pretty potent right click damage.
Razor: against solo targets, with aghs, his armor reduction is unmatched, being able to reduce armor by upwards of 70 points. His damage drain isn't that strong in the late game, but it is still essentially free damage to you while slightly reducing the damage of the bosses. Also with octarine core, his ultimate has like a 5 second down time on the final level.
Outworld Devourer: Due to having a lot of items which greatly increase intelligence, his arcane orb deals insane damage per hit. With octarine core, this results in a lot of healing. It's also pure damage, so the insane amount of armor and magic resistance that the bosses have is meaningless.
Earthshaker: Enchant totem. Hallowtide rapier. Deals like 3k damage a hit. Add in daedalus for insane damage potential. Also he is capable of stunning Medusa for a very long time while he deals this insane physical damage.

Go Silver edge, it is really easy. Go invi each time she ults, break her evasion when her ulti is over.

For hitters, a butterfly or any dodge, an mkb and a bkb.
For casters/supports, a sheepstick, orchid and halberd. :P

Me and my brother finished the game easily with Necro and Enchant :)