I think South West Trains was the last other than GNER and the Caledonian Sleeper.
With other operators I think it was First Great Western (2000), Virgin Trains (2001), Midland Mainline (2003), Scotrail (1995 but local Strathclyde 1989), Reginoal Railways and Network South East (1990-1993), Northern Ireland Railways (1997), Wales and West (1998), Eurostar (2001).
National Express East Anglia were amongst the last as well on the Norwich-London hauled stock. I believe that went in 2004.