1990-91: 420SEL (W126)
1992: 400SE (W140)
1993: 400SEL (W140)
1994-99: S420 (W140 until 1999, W220 in 2000)
2000-06: S430 (W220 until 2005, then W221)
2007-14: S550 (W221 until 2013, then W222)
There's a strong correlation between the quality of the Mercedes and its real value. The W126 was solid. The first few years of the W140 were awesome, and then Mercedes started cutting costs. The W220 is arguably the worst S-Class, and it shows with its relatively low price.
Sources for Merc MSRPs: AutoTrader, CarGurus, and BenzWorld