While the results can be the same, they sometimes are not - abd the result depends on the situation and images. When you have trouble blending a transparent GIF looking right with your background or when the matching technique yeilds a color that is slightly wrong, it may be that you are choosing to is difficult or that you are choosing to do it with the wrong method. Learn both techniques, and understand how to use them so you increase your ability and chances of success.
I personally tend to use the blending technique more often than transparency. The reason for this is that GIF transparency tends not to blend well along shaped edges or for things such as drop shadows, and often one or the other of these is present in my graphics. On the other hand, if you are floating an image over a textured or complex background, you really can't do that too successfully with the blending technique. This might require more clever use of matting (See "Forward and Back" for more discussion on matting).
Keep in mind there are other techniques for accomplishing what you want on the web as far as the positioning of graphics is concerned. While a floating graphic may seem like a cool idea, sometimes combining the images you want in Photoshop and/or deploying images in set positions using tables and layers (browser layers, not Photoshop layers) might work better.