Yes emissivity does greatly effect the temperature readings given by thermal measuring devices.  Emissivity is in fact the way that an object gives off its radiant energy.  It must be calculated for to recieve accurate temperatures.  Most of the time if you leave the setting the same (1.0) throughout an inspection the data can be compared to itself (qualitative thermography) this means comparing like componants with like loads to each other.  Very rarely am I asked to take accurate temperature readings (quantitative thermography) this is expensive and takes time.  It all depends on the type of inspection and the time allowed for the work to be completed.

So for these IR temp measurements devices of the shelf, they are assuming the emissivity is one? The results of a measurement would be very repeatable just not entirely accurate? How would you do quantitive thermography if you don't know the emissivity? (not possible?) I am thinking of the generic IR devices that are not built for any specific material. Thanks for the post.

To Buzzp
Imagers with the capability of adjusting the E are typically set at 1 by the qualitative thermographer.  Contact radiometry and spot radiometry may or may not be set at one.  Typically these instruments are set at .96 or .97 because this most closely associates with the E of organics and allows for a little more accuracy.  Check on the specs to ensure you are getting what you want.  Be cautious about E tables as they serve to be close but each imager by model and even in some cases serial number will interpret E differently.  Refer to the ASTM Standard E 1933-99 for details on deriving/compensating for E.  Do not forget about the Reflectance and Transmittance errors when working towards your most accurate temperature.
Good Luck

Thanks for the info!

Your question about Accuracy when performing a Qualitative scan is answered by considering that you are using the same instrument to measure relative temperature differences within the same image background(in most cases).  Two schools of provided comparison of like data are commonly used by todays thermographer.  The first compares a suspected fault to a background(like the cabinet) temperature within the same image and the second compares the suspected fault to an assumed similarly loaded component(like connections on C phase with the suspect fault on similar connections on A phase).  In both cases you assume your instrument to be in cal and as such, linear in error.  Your temperature difference between the two compared points should have only instrument and cal errors between them(assuming like components have a like E, no reflection and similar transmittance errors).  This temperature delta is reflective of temperature difference under similar conditions and, with the same instrument, are fairly accurate representations of that difference temperature.  Remember that in qualitative thermography you are providing a difference(delta) between two points(Qualitative) and not a temperature based on a reference point(like the freezing point of distilled water or absolute zero), A Quantitative figure.

Emissivity of shiny objects (such as copper bus and many copper connectors) can be very, VERY low (.05).  This means that your temperature reading using a handheld spot radiometer might read 60 degrees C whereas a contact thermometer might read 260 degrees C!  As there are published guidelines to maximum allowable operating temperatures for electrical equipment, a significant temperature reading with a spot radiometer should sound an alarm in your head!  Do not count on temperature readings as a measure of criticality of a noticed hot-spot.  There are a number of factors that should be considered before walking away from a possible problem.  Check out www.snellinfrared.com for thermographic issues and tips.  They are very knowledgable.

You can guesstimate the temperature errors resuling from  emissivity errors by considering that the energy flux F ~e*T^4 where e is emissivity and T is temperature on an absolute scale.

So a 10% error is e equates to approx 2.5% error in T. If you're looking at something that is 100F actual that equatest to approx 14F.

ie if it had actual emissivity of 0.9 and you dialed in 1.0 your gun would telll you that it is 114F.

Another big source of error has to do with the "spot size" for guns and camera's.  They will average all the temperatures over a certain spheradian field of view.  If you move farther away from the target that area increase. If your spot size is 8 square inches and your target is 4 square inches, you will likely end up reading a temperature about half way between the target and the surrounding temperature.

A piece of Scotch "88" electrical tape has an emissivity
of .95. Stick a piece of it on whatever type of material you
want to measure , set the emissivity to .95 and take a reading. Measure just next to the tape and adjust your emissivity 'till the same temperature is indicated, you now
know the emissivity for future reference.
Dont forget about background (not ambient air) temperature,
the lower the emissivity the more influential the background
temperature is.