IR Thermometers read surface temperatures. Can they accurately read the interior temperature of my oven through the glass panel? Or will it be reading the surface temperature of the glass rather than the interior?
It will measure the temperature of the glass itself, but not necessarily in an accurate way. Most glass is largely opaque to IR, but will radiate IR of it's own based on temperature.
The trick with IR thermometers is that they are guessing the temperature of an object by making an assumption about how much IR (Infrared Radiation) that object will radiate when it is a certain temperature. Cheaper IR thermometers have what is called "fixed emissivity", which means that they always assume that the object you are measuring is radiating 95% of the radiation that it would theoretically emit if it were a perfect black-body object. An emissivity of 95% (or 0.95) is a good start for most household objects - cloth, painted surfaces, etc.
Where it breaks down is with things like shiny metal, glass, liquids, etc. For those objects, the amount of radiation released at a given temperature is more or less than the expected 0.95. Shiny metal pans, for instance, can be as low as 0.2, meaning the displayed temperature will be much lower than the actual temperature.
You can use tables of emissivity values to correct your temperature reading, like here: http://www.tnp-instruments.com/sitebuildercontent/sitebuilderfiles/Infrared%20Thermometer%20and%20Emissivity.pdf (Note, for this table, use the 8-14 micron column).
That takes away most of the convenience of the thermometer, but it is a useful reference. The closer an object's emissivity is to 0.95, the more accurate your thermometer will be. You can improve accuracy by painting an area flat black, or even using a piece of masking tape stuck on the object to make a good "reading point". Fancier thermometers allow you to set the emissivity, and even fancier ones allow you to auto-calibrate with a contact-thermometer add-on.
To get back to the original question, glass has an emissivity of around 0.75-0.85, meaning the measured temperature will be a little lower than the actual temperature. Of course, even an accurate glass temperature doesn't tell you a lot about the actual oven temperature. My favorite surface for taking the measurement is my pizza stone, which is just about 0.95, perfect for accurate readings.
Don't try to use IR to read "through" a glass window. While an IR thermometer's target indicator light can be transmitted through glass, the actual "read" will be of the glass surface and surroundings rather than that of the target on the other side of the glass.A handy "workaround" technique that will give you an approximate reading of a case's internal temperature is to flip open the case top or front and quickly take a reading from its inside surface, which should approximate the temperature of circulating air in the case.
Understand your instrument's "field of view." How much of a target an IR instrument takes its reading from is also important. Some units use a light emitting diode and lens to cast a flashlight-like illumination over the actual target area you are measuring. Others use a laser dot that indicates the center of the target area, but not the boundaries. (Food Management)
To make use of your IR thermometer, be aware that "They will not measure polished surfaces accurately, or measure through glass, because glass can block infrared radiation. To measure such surfaces, stick a piece of flat finished adhesive tape to the shiny surface ... and point your thermometer at the tape. (Fluke)"