I usually use computer lettering, although for titles and effects, I've been increasingly utilizing a combination of hand and computer lettering. For regular word balloons, captions, and occasional effects, it's a lot quicker, and there are plenty of fonts available. Effects done on the computer can look very slick and seamless.
The drawbacks I find to computer lettering are that the selection of fonts can be overwhelming, and in one case, I sent a comic to print having used a font that really wasn't up to the task. Since then, I've committed to using maybe the same three fonts for labels, captions, and word balloons. Because if a font has the right balance of dynamism and legibility, why change it? Also, it can be too easy to get carried away with lettering effects and sacrifice legibility, yet at the same time, there are only so many things you can do with computer lettering effects. These limitations don't apply to hand lettering.
The only drawbacks with hand lettering I see are the time it takes, the mess it can make, and how hard it can be on my hands. But with a blend of hand and computer lettering, I figure I get the best of both worlds.