This applies to all races but essentially letz say you manage to get a few of your units right in the middle of his base, which building would you go for to cause the most damage/inconvenience to his war effort? (as his enemy frontline force struggles to return to base to defend it)
I present a example of a SM base (wrong most probably) below.
**Remember this is a TOTALLY WRONG example but just to show you how your line of argument can be laid out I came out with some fictitious text **
Killing his HQ reduces his req by -15 and disables his ability to build and USE (if already owned) the Relic and droppods. Building this building again from scratch is no small feat. NOTE: If you destroy the HQ BEFORE the machine cult comes up, all Armory research is cancelled and the Armory is disabled too.
Take less than a minute to rebuild. Not really worth it as (see above and below) there are more higher priority buildings to take out.
If he has more than 3-4 power generators grouped together, you can possibly gun for these to hammer his production of Dreads and other machines. Note to watch out for Thermos if he has any.
NOTE: Look for clusters of 3 or more generators together. Destroying two will automatically take out the third one from the splash damage. This can be done relatively fast.
Killing an SM armory accomplishes 3 things.
One - he drops back to only two heavy weapons per squad.
Two - the targetting module upgrade is reduced back one level and
Three - The Relic building is disabled (but not the War Factory).
Note that Bionic upgrades stay researched even if you destroy the Armory. Overall a good 2nd choice as it will effect ALL marine and terminator squad weapons and accuracies. NOTE: If a squad already has four weapons, they stay that way, but if the squad gets wittled down, they will only be able to build up to two heavy weapons maximum.
Lots of hp, difficult to kill but aim for this if you need to stop the flow of dreads and other vehicles. Note that though this may seem a wise decision, it is overweighed by the sheer quickness of rebuilding it. Gun for the Armory or HQ as a better option.
Don't bother with this as research upgrades still stay researched if you gut this building. Power gens and the Armory are a wiser decision.
SPs and LPs
If you see an uncapped SP, take the time to decap it. You only need eight seconds and this will set him back a bit. Normally 2-3 SPs can be found near his base. However if having to choose between two SPs and an Armory, go for the Armory for the reasons mentioned above.
In all for SMs, the most 'inconvenient to your enemy' building to destroy is definitely the HQ, as a lot of effects flow down from there, and it takes a darn long time to build. Second choice would be aiming for his armory or power gens if you can make it. If your attacking force is really weak, just take out a power gen if you can.