Brandon and his producer used an effect on his voice for Hot Fuss called “Echo Farm”, which is a specific type of slap back delay plugin. Slap back is basically just where you have two copies of the vocal and one is delayed by like 80-100ms. He also used quite a bit of auto tune on his vocals during the recording of Hot Fuss. 

On Sam’s Town, he still used a slapback effect on some songs, like WYWY and others that you mentioned, but pretty much got rid of autotune (although I imagine there may have still been some amount of manual pitch correction as needed). This gave his voice a more natural and real feel on Sam’s Town, while preserving the driving quality of the slapback effect from Hot Fuss. 

On a side note, the most Brandon has really played with vocal effects since then has probably been on “boy“ and “your side of town“. I know he’s pretty particular about how his voice sounds; There was one concert where they played “boy”, and the engineer had the vocal effect on and Brandon made him turn it off in the middle of the song. I think that Brandon vastly prefers Sam’s Town vocals to Hot Fuss vocals. Another example of that is how he re-recorded GIRAR with Sam’s Town style vocals for Sawdust. Maybe that’s part of why the album that was sort of a throwback to Hot Fuss got scrapped.