I am back into my research mode for an S and am wondering about experiences with '03/'04 both new and used. I have checked on e-bay and autotrader (like seeing the actual sales though).

Don't know the exact options, but I have seen them sell in the high 40's for '03. Lowest '04's in low 50's

 

I am guessing based on your numbers that those were very lightly loaded S models.
Generally $4-5K off MSRP for new cars independent of options (except air suspsension). I was offered $8-9K off of MSRP for an absolutely loaded S model with a few K miles (dealer loaner/demo).