First off you should know something about the images. All the programs use the same databases, for example the Palomar Deep Sky Survey for visual data, and the IRAS survey for infrared images. There are (very) minor discrepancies in the location and appearance of objects between the three programs due to they way the images are digitized/compressed and stitched together, but they are using exactly same images.
Another thing to remember is that the DSS plates date from 1956-1958 (yes, that's right), and the IRAS images date from 1983. So they reflect the sky situation decades ago. Nonetheless, the sky revealed by these images can be quite astounding.
Take for example this image of a bright, angry looking object in the IR view of Google Sky (right image, also seen in world wide telescope and wiki sky, search on the following coordinates 09:47:27, 13:16:27), absent from the visible light view (left image).
This object is now being touted as comet Elenin, a while ago it was being touted as Nibiru. In fact it is is the carbon star CW Leonis (also known as IRC +10216, PK 221+45 1 and the Peanut Nebula). CW Leonis is the brightest object in the 10 μm infrared sky, and well known to experienced observers. But if you are new to the field, it can look quite mysterious.
It is an artifact, a vagrant blob of light on those plates, there's a few of them on the larger image (and some edge artifacts from differing exposures between the plates as they stitched the images together, Google sky uses a different approach to compressing the images, so the object and the other artifacts look slightly different). Despite being one of the best instruments of its time, the 48 inch telescope at Palomar Observatory did not always take perfect images.
A nice example is this image near Spica in Virgo, where you can see an image of the primary mirror in the picture just above Spica (the bright star in the target box).
As well, while the Palomar survey was roughly only 99% complete, there are some areas where plates were not of high enough quality (or don't digitize well), some of these blank spots are claimed as "cover-ups", but just represent areas of data loss for one or more reasons.
Similarly, the IRAS survey was not complete (around 96% of the sky), and there are a number of missing frames where images weren't taken, or the images were defective.
So while the virtual telescopes can give us unprecedented views of the sky at multiple wavelengths, what you see can occasionally be difficult to interpret. Before rushing off to claim comets or brown dwarf stars, take a bit of time to become antiquated with astronomical objects, and the characteristics of the images. You may learn something wonderful.