For the sake of this article, we are going to start the conversation out assuming that GW will rule against being able to affect embarked units.
That being said, this is still a very effective unit and when used properly can wreak serious havoc amongst your opponent.
The first thing we need to talk about with the doom are his weaknesses.
1. Synapse - Despite what you may think, this creature is not a synapse creature and can revert to instinctive behavior. His leadership is a 10 so the odds are very small that this will happen, but it is something to keep in mind. He uses the instinctive behavior feed and will basically assault the closest thing to him, foregoing his shooting attack if he fails a leadership test.
2. Toughness 4 - Power fists, Thunder Hammers, force weapons, melta guns, las cannons, and most artillery will instantly destroy a Doom no matter how many wounds he has. All it takes is one failed 3+ invun save.
3. Mobility - If an opposing army moves away from the doom before he has a chance to soak up any wounds, he is a walking shadow of the warp and not much else. If this happens, I will typically seek out some of my other squads and use him for support.
Ok, now that you know the weaknesses of the doom, let’s talk about how to use him effectively.
There are several types of deployments that an enemy will choose that will benefit the doom, so in my opinion the best way to use him, is put him in a spore pod and drop him "post" deployment. If you are dead set against using pods, you can always use the hive tyrant ability and outflank him.
What you are looking for is exposed units that are either in cover, or are marching forward. I typically drop the spore pod 1 inch away from anything dangerous and then hope for a low scatter roll.
Once he drops in, you want to position the unit as close to the enemy troops as possible, while getting as many units within your 6 inch bubble as you can. If you are lucky enough to get close to large infantry unit without a powerfist or other str 8 weapon, you are advised to immediately assault that unit. This will protect your doom from reprisal from lascannons and melta shots during the enemies shooting phase and still allows your doom to soak up wounds from the engaged infantry unit during both shooting phases.
Also don't forget that once you get 8 to 10 wounds to start punishing tanks during your shooting phase with that str 8 to 10 AP 1 cataclysm. The range is very good on this weapon.
Finally here is a breakdown by army of how I have best used the doom
Doom vs space marines - Devastator squads, sternguard in drop pods, scouts, assault squads and exposed tactical squads will die in droves to the doom. keep yourself in assault so you don't get rapid fired down.
Doom vs eldar and dark eldar - I personally will drop the doom right into a farseer council. Yes, I might die quickly, but I am almost certain to get my points back. Eldar do not have a ton of high str melee weapons so almost any infantry will fall to the doom. I have yet to play against dark eldar so I don't really have alot to say on that.
Doom vs IG - Ahh yes, command squads, heavy weapons teams, large veteran squads, almost anything IG will fall to the doom.
Doom vs chaos space marines - This guy is really good at taking out squads of obliterators, Khorne beserkers "might want to stay out of melee there" and especially plague marines.
Doom vs chaos demons - This one is a bit tricky as the deployment of demons is never a sure thing. Just look for soft spots, or use the doom to try and leech a few wounds off of a demon prince before he wipes you off the board.
Doom vs Orks - This guy is great if dropped right into a nest of nobz or even mass amounts of boyz. Now, he will probably get dropped though if he gets assaulted by by 30 boyz, but he might take 15 of them out with him. Try and drop him next to lootas and burners though and they will pay big time.
Doom vs nids - If you can find a large group of termagaunts, this guy is awseome. just assault them and they will feed you for multiple turns, forcing the nid player to always be looking over his shoulder. Also if you can find hive guard sitting by themselves, or biovores, he's great, because they only have a 7 leadership. Stay away from large groups of hormagaunts with poison glands though because you won’t get your points back.
Doom vs necron - I think that this is where the doom is at his peak since necron has no mechanized units to speak of. Just be careful not to park him next to a unit of guys only to have them get sucked into a monolith leaving you all by yourself.
Doom vs Tau - Crisis suits. OH MY GOD. I love to kill crisis suits with the doom. nothing pisses off a tau player by having a doom drop into the middle of his turtled position and he can't do 10 wounds back to you. I have tabled tau players in 3 turns with 1 doom dropping into this ranks.
I hope this helps you in your gaming. Have a good one.