On my Samsung phone with Jellybean in the call logs. Each call, whether outgoing, incoming or missed, on each entry there's a little coloured rectangle(shaped like a SIM) with a number on it...1 or 2 depending on which SIM was used, and different colours for each SIM as well. Another phone I've got with ICS it's very similar, but shows the name of the carrier, rather than 1 or 2 in the coloured rectangles.
That's for ICS and JB, I presume there's something similar for Gingerbread, etc.
Also in SMS it's very similar, SIM shaped rectangles indicating which SIM was used for a particular message.