So if I got a weapon that gives me bonus poison or elemental damage and/or bonus skill damage to a skill which I use, is this taken into account in the added/substracted damage rating of the item?
No its not. If you notice, those slots have an orange diamond on them meaning they aren't taken into account for comparisons.
However, those stats will now show up in your detailed character sheet.
Bonus skill/elemental damage is not calculated into the shown DPS. All bonus skill/elemental damage have an orange indicator in front of it. And this means they are not included in your shown DPS.