There is a lot that can instant death the Doom.
Infantry that cause Instant Death to the Doom:
Cryptek with Eldrich Lance (S8 AP2) - can have up to 10 in an army.
Heavy Destroyer with Heavy Gauss Cannon (S9 AP2) - can have up to 9 in an army.
Necron Overlords with Tachyon Arrow (S10 AP1) - can have up to 2 in an army.
'Some' vehicles that can 'instagib' the Doom:
Doom Scythe Death Ray (S10 AP1) - up to 3 in an army.
Doomsday Ark Doomsday Cannon (S9 AP1) - up to 3 in an army.
Triarch Stalker Heat Ray (S8 AP2) - up to 3 in an army.
Monolith Particle Whip (S8 AP3) - up to 3 in an army.
Monolith Portal of Exile (removed as a casualty) - up to 3 in an army.
Then there is also the C'tan Transdimensional Thunderbolt (S9 AP2) - up to 3 of these in an army.
I think it is pretty ignorant to say that The Doom is 'unkillable' by the Necrons.
Well lets take a look
The Eldritch Lance is a very common item, if I had to hazzard a guess you can easily see at least 3 per army. While not every army will utilize Crypteks enough do that it is something to look at. Considering most people will place them in Night Scythes you don't have much to fear as they would need to disembark, however if your opponant is the Ghost Barge type of guy they can of course shoot from saftey. All in all unless your opponent is spamming troops or are spending on double courts you have only to deal with 3ish on average leaving you LOS blocking tactics or trying to CC or just passing your 3+ save. If you get Iron Arm, you of course can ignore the Lances.
Heavy Destroyers can indeed pose a threat but not many people take them, those that do certainly don't take 9 (thats almost 600 points by themselves) Unlike the Lance weilders above the Destroyers cannot hide in Vehicles and large blobs of troops, the Nid player (on average) has the tools to deal with a unit or two containing Heavy Destroyers, just dropping nearby the Doom can kill off the whole unit, removing that threat neatly. Now that I actually think about it DO people even take HD's anymore? Of course if you get Iron Arm you can Ignore the Heavy Destroyers.
Lords with Arrows are semi common, TBH I think most Necron players would rather take a kitted our Lord on a barge or a Destroyer lord for some wraiths. However if you do run into a Tac Arrow you can be confident in the fact you would not have to face the threat every turn. Unlike a lance that has to be dealt with until killed if they Miss, fail to wound, or you pass your save you are A-Ok afterwards. The chances of you facing more than 1 arrow are slim, and frankly if they spend 60+ points on grabbing two arrows they are taking away from the rest of the army. Again as always if you get Iron Arm who cares.
Now Death Sycthes are a very real threat, as mentioned in my previous post mostly only vehicles will have the punch to reliably threaten a Doom consistently. Really you just want CC or to pass your 3+ invul save to avoid them. Most people will run 2-3 at least so unless the rest of your army poses a large threat they will be gunning for you. You can however (assuming going second) simply deploy away from them buying anywhere from 1-3 turns while they maunoever into firing range. Again Iron Arm = Auto Win
Now on the subject of Doomsday Arks, personally I wouldn't run them as I prefer a much more mobile aspect to my army when required, however a lot of people enjoy the unit so you can easily expect to see 2 on a good day. Now because of the points cost of the Death Scythes and the Arks you generally won't see more than 4. While the Nid player has the tools to easily deal with AV 13 open topped (see Venom weapons and Rupture cannons) the Doom also can pop them easy. While you do have a 3+ to save you, mostly I wouldn't worry to much since that blast will have a hard time hitting the Doom itself. On average it only needs to scatter 2.5-3 inches to avoid hitting the doom (average roll is 7 and BS is 4 so yea..) meaning you have VERY good odds of not even having to make the save. I'd say a Ark (assuming they are not shooting the rest of the army) is a 50/50 threat while simply deploying LOS blocking tactics will nullify it completely.
The Stalkers are a very dangerous threat to the Doom simply for the fact they can hunt it down and fire Twice. Mostly the firing twice bit. Its tough to save how many of these you will on average face, if it was me I would like to run two, most people will not even run one. Basically you have LOS blocking tactics and CC to reliably protect you, but making two important saves in a row does not have favorable odds, especially if they make you do it often. As always Iron Arm doesn't care. Really though chances are you will not ever fight these, despite them being actually very awesome.
Particle Whip, yea we know these exisit but lets be honest, who runs the Monolith anymore? Its not a bad model but is simply outclassed, while relying on a paper/rock approach does not make for good list building, if you were to see more than 1 in a list it will be a very rare day. Having 3 in a enemy list dreastically changes the way the necron army will fight actually making it easier on avergae for the Nid player to win. the 24' range is a real killer though allowing the Doom to out mauncover the Tank and employ LOS blocking shenanigans.
Yes the Portal, really? Other than getting close by Deep Strike has anyone ever seen this happen>? If you have Iron Arm you have a excellent chance of making the STR test, otherwise simply deploy the Doom elbow deep into the enemy army to prevent the Monolith from being able to deploy close to you. Most people do this with the Doom anyway so its not asking for much.
Yea C'Tan do those guys even exist anymore>? The Trans Bolt is a threat but A) someone has to take a C'Tan when could could take ANYTHING ELSE, and B) this someone would have to pay the large point expenditure to take the power. Lets be honest, everyone is different and enjoy different playing style and armies, but I don't think other than maybe once you will ever seen a C'Tan with this particular setup. If I had to take a C'Tan I would take more utility powers like the Deepstrike defense and use him as counter charge.
Since the C'Tan is not immune to the Doom simply deploying him close and even assaulting is a worthwhile counter, also Iron Arm.
So what have we learned? On average you will basically only have the Lances and the Death Scythe to worry about. While I can see the more extreme lists having 4-6 Death Scythes, against a complete Flyer Force the Doom would be of limited help anyway. Against the more traditional and balanced Guass/Telsa combos the Doom the devastating. In those rare situations where the player has 1-2 units of all the above, remember spending 1+ turns firing everything he has at the Doom is a effective strategy by itself, as he could easily be spending close to 1k points to handle a 90ish point model. Leaving the rest of your army room to advance with impunity. I don't know about you but I would spend 90 points to become immune to shooting for 1+ turns.
The lower in point you go the less tools the Necron player will have to deal with the Doom making him more and more valuable. Combo with Deathleaper for lulz.
While the LD 10 can "Slow" the doom down it will not stop him, as per any army, you need to handle the doom before he gets his momentum, once he starts sucking wounds (either through his ability or through Spells) he is basically unstoppable
Also Iron Arm = Lulz aganst the entire Necron Army.