When I first got Fallout 3, I thought the voice modulation the power armor helmets add was a nice touch.
For the longest time though, it's been removed from the game.
My only question is why? Is there a way to enable it via mod or ini tweak or anything?
This may be a mod you have running. Voice modulation is an option for wearable items; usually used on power armor helmets.
You can try running a game with no mods... and click past the "missing content" warning, and see if they speak with modulated voices. Don't save your game or cause it to auto-save.
If it works... Its one of your loaded mods.
The option can be altered using the GECK. Once you know which mod, you can fix it ~or if you can't find the mod, you could possibly make your own and load it last.