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Real line of sight rule is good and dandy but sometimes leads to confusing situations.
Lets consider a building, with wide windows, such as this:
http://fc08.deviantart.net/fs71/i/2011/326/5/2/ogrin_house_by_namezong-d4gxptb.jpg
Now its windows are large enough that you can see through windows inboth front and rear wall, as this photo shows:
http://fc09.deviantart.net/fs71/i/2011/326/2/1/ogrin_house_5_by_namezong-d4gxqi7.jpg
Can you thus shoot at the target on the other side of the building that you only see through the building's windows?
Raw seems to say yes, but it sounds outright ridiculous if you can't shoot embarked unit (see through one wall's window) but can shoot unit if you it through two walls' window.
Help?

Yup. but be prepared for hefty cover saves as well as LOS-limited casualties.

 Ratliker wrote:
Real line of sight rule is good and dandy but sometimes leads to confusing situations.
Lets consider a building, with wide windows, such as this:
http://fc08.deviantart.net/fs71/i/2011/326/5/2/ogrin_house_by_namezong-d4gxptb.jpg
Now its windows are large enough that you can see through windows inboth front and rear wall, as this photo shows:
http://fc09.deviantart.net/fs71/i/2011/326/2/1/ogrin_house_5_by_namezong-d4gxqi7.jpg
Can you thus shoot at the target on the other side of the building that you only see through the building's windows?

Yes, as long as you can see the target unit your model can shoot at it. True Line of Sight is used at all times in 40K.

Raw seems to say yes, but it sounds outright ridiculous if you can't shoot embarked unit (see through one wall's window) but can shoot unit if you it through two walls' window.
Help?

You can not shoot an embarked unit because they are not on the table and therefore can never draw Line of Sight to them.

If you can see it you can shoot it. Passangers are never on the table, so no LoS can be drawn.

Except when embarked in buildings...

 Kevin949 wrote:
Except when embarked in buildings...

ummm, buildings are treated exactly like vehicles. You can't shoot their occupants either, except for grenades or flamers through the firepoints. But thats an explicit exception.

 Grey Templar wrote:

 Kevin949 wrote:
Except when embarked in buildings...

ummm, buildings are treated exactly like vehicles. You can't shoot their occupants either, except for grenades or flamers through the firepoints. But thats an explicit exception.

Exactly this.

However if it was a ruin instead of a building the models would be left in the ruin and True Line of Sight would apply as normal.

 Kevin949 wrote:
Except when embarked in buildings...

No. You're confused about the embarking process in buildings. You don't physically place units inside the building. They are taken off the table, just as if they were embarked in a vehicle. The exception to this is if they are on the battlements(top) of a building, in which case they don't count as embarked and can be fired upon.

If you're using custom-made buildings that you place units physically inside, the easiest way to handle it is to simply call them ruins and use the rules for them instead of using building embarking rules. This would mean you can still fire on them with true line of sight, as you should if you're keeping them on the map, physically inside a structure(ruin). Building embarking rules were specifically made to give rules for GW fortifications, not so much fan-made buildings.