Appearance is a relatively small part of a beer's score on a BJCP score sheet, but it is very important. There are generally 3 things to look for: color, clarity, and head (retention, color, and texture). While only 3 points are available, presentation is very important. If a beer doesn't look right, it can influence your whole experience. If Aroma sets the stage for your experience, Appearance seals its fate. Personally, when I evaluate a beer, I tend to consider both Aroma and Appearance at least twice. I will try to jot a quick blurb while the beer is pouring, get some quick sniffs for some more volatile aromatics, and then revisit both.
Color is a big part of style. All styles have an acceptable SRM (Standard Reference Method) range. A brown pilsner or a blond stout is simply not something you expect (despite the experimental styles that are becoming more common like Black IPAs). Generally speaking, the combination of color and aroma is going to 'color' your expectations. Generally speaking, lighter beers (in color) are going to be different than darker beers that use darker or roasted malts.
Clarity is also a big influence on what to expect. Generally speaking (with obvious exceptions like hefeweizens), clearer beers are better brewed beers. Also, certain types of clarity issues can point towards process flaws. For example, chill haze is a condition where a beer looks cloudy when cold, but can be brilliantly clear when warm. It's caused by certain proteins which remain in suspension in the beer that show up when cold. There are numerous ways to reduce it, from a vigorous boil, to using finings (either pre or post fermentation), to rapid chilling, etc. Clarity can also point to things like young beer which hasn't sufficiently aged to signs of infection. A handy tool here is a small flashlight. Shine it through the glass on darker beers and it will help you determine clarity and color (or how opaque it is).
Head has several properties which vary from style to style. Retention is how well it maintains its level after a short period of time. Generally, you don't want it to completely dissipate, but some styles will dissipate more quickly than others. Retention can be aided by using some non-fermentable proteins or sugars, as well as hop additions. Generally speaking, 1/2 pound of dextrin or carapils malt either steeped or mashed per 5 gallons help. Most unmalted grains (wheat or flaked barley, for example) will have the same effect. Don't overdo it, though, because too much will cause chill haze. Color can range from white to deep brown. Finally, Texture is important too. Generally speaking, fine bubbles will appear creamier and will look more appealing than large coarse bubbles (or even worse, no bubbles at all).
In conclusion, although it's only 3 possible points on a BJCP score sheet, pay close attention to the Appearance of your beer. With beer, it's acceptable to judge a book (at least partially) by its cover.