Considering that hot air rises, near the top of the case is the optimal location to measure the highest temps. If you do a lot of work with a CDRW drive (in the top of a tower) put it near the lower rear of the drive. You could also experiment with different positions but just keep the thermistor away from a fans direct air flow, it may give you a false indication (lower temp reading than actual). This is a good way to discover any devices that would need additional attention for a fan.
Also any area that is in a 'dead airflow' area (blocked by the flat IDE/SCSI cables) is a prime location for running hotter than an adjacent part of the case.