Linked to this forum from another location and this post caught my eye.
I had a customer at work (I work at Best Buy as a tech) who had this same exact issue.
The cause was his Antec SmartPower. It has a fan that stays off until the temperature gets high enough and then it kicks into gear. It happened only in Doom 3 and it happened at the exact moments that the fan became louder.
We swapped him into an Antec TruePower where the fan is constantly on (albeit perhaps not running at full strength) and the issue was resolved.
Check if your power supply has 'quiet' technology and see if it can be disabled.