Geological methods: Interpretation of facies and other clues in sedimentary sequences. Evidence for measuring the rate of change in the carbonate compensation depth (i.e., as this changes the area for deposition of carbonates changes also producing changes in the proportion of this rock type within marine sedimentary deposits). Any change in ocean temperature, pH, pressure (depth), atmospheric concentraions of particulate matter, biodiversity, should be reflected in the stratigraphy (facies). In the same way one interprets if a turbidite sequence is proximal or distal by sequence and relative thickness of beds. Tucker and Slingerland 1997 ftp://ftp.geosc.psu.edu/pub/geosc/sling/PDFs_of_pubs/Tuckeretal1997.pdf
Geomorphological, geological, paleobotanical evidence (Buck and Monger 1999 - http://faculty.unlv.edu/buckb/Buck%20Publications/Buck%20and%20Monger%201999.pdf
(Lambeck et al., 200? Nature - http://studentresearch.wcp.muohio.edu/ClimateChangePrediction/climate_sea_level_chg02.pdf), Anything by A. Nuemann and P. Hearty on evidence for sea level change during interglacial preiods (the Bahaman islands, etc). Not my expertise but there has been much work done in this area.