I'm actually interested in the perception of time in animals, but it's not my area of expertise -- just something I occasionally read about. You could try looking at the work of Dr. Angelo Santi of Wilfrid Laurier University. He does experiments on both pigeons and rats. http://legacy.wlu.ca/page.php?grp_id=273&f_id=1&p=18886

Dear David, 

I have done a lot of learning with mice. Mice like rats differ within strains as well as in their general capacity to learn e.g. a linear maze and thereby in their use of time. This is a problem when you calculate your results and have only a few animals in your group. They also differ in their natural activity level; our mice were most inactive about 9.30 AM. 

You can use a temporal discrimination operant task in rats (see link below).  You train the rats so that, for example, if a tone comes on for 2 seconds they press a certain lever for a reward, but if the tone comes on for 8 seconds they press the opposite lever for the reward.  Other operant tasks also have a time perception component to them.  For example, the DRL-72 task requires the rats to wait 72 seconds before pressing the lever for a reward.  You could also adapt this task to change the DRL requirement to different times based on different cues.  The delayed discounting task also has a time perception component to it, as the longer the time for the delayed reward is perceived, the less valued the delayed reward will be to the animal.

http://www.ncbi.nlm.nih.gov/pubmed/12880908