Perhaps grades aren't needed
Some instructors don't grade clicker questions on the basis that engagement is the classroom norm expected of all students. In particular, if difficult "ConcepTest" type questions are used, for which 30% - 70% of students are expected to get the answer wrong, it may be difficult to grade clicker answers. Some research finds improved student discussion if clicker answers are graded on a low-stakes basis (any answer given credit, not just correct answers.)
Strategies when using clickers the first time
You may want to adopt some sort of "do no harm" grading policy the first time you use a classroom response system. You don't want a student's grade to be lower than it would otherwise be simply because of your lack of experience with technology. Some instructors have experimented with different grading weights and procedures as well as delivery methods before finding a set of procedures that is efficient and work well. Give yourself one or two semesters to experiment with your style and grading before settling on your preferred one.
One grading policy is to have the clicker points as extra credit. You should find significant participation with only 2 or 3% of the course grade offered as extra credit with clickers. This policy will take the pressure off you and the students to quickly climb the learning curve and "get it right" the first time. This policy can be particularly attractive if clickers are new or seldom used at your institution. You may encounter more difficulties if both you and the students are unfamiliar with the technology.
Another grading policy is to have the clicker points reduce the weight of one or more exams, particularly the final exam. Suppose you require a comprehensive final exam worth 30% of the course grade. You could allow a student to earn a small portion, say 5%, of the final exam score as clicker points. If a student earns zero clicker points, their grade is calculated as originally described and no harm is done. If a student earns some clicker points, then part of the final exam is earned early instead of on the exam itself.
Another grading policy is to have the clicker points substitute for some other assessment. Suppose you require homework or quizzes worth a relatively small portion of the course grade. You could allow a student to earn clicker points that count toward or replace some of the homework or quizzes.
If you elect to make the clickers mandatory and count as part of the student's course grade, you should consider weighing the clicker portion as a small percent so the student isn't adversely impacted just because of inexperience with technology. As you, and they, become more familiar and confident with the technology and delivery, you can increase the weight accordingly in future semesters.
Strategies for experienced users
A good general grading principle is to have some sort of forgiveness policy with regards to clickers. One such policy is the grading of each clicker question. Award some points for any answer (to encourage students to answer even if they don't really know the answer) while awarding some higher point value for correct answers. That way a student is accumulating points simply by answering the question. Then assign the clicker portion of the grade by ignoring, deleting, or forgiving a certain number of questions or points.
For example, award 3 points for a correct answer and 2 points for an incorrect answer. At the end of the semester, assign full credit for the clicker portion of the grade if 67% of the total clicker points are earned. That way a student can answer every question for the entire semester incorrectly but still earn full clicker credit. Most students won't answer everything incorrectly. Therefore missing one question during any given class period or missing an entire class period won't drop the student below 67%. You can politely dismiss the student by explaining that missing some questions won't harm their grade. A more detailed grading policy is offered on Joe Calhoun's syllabus (Acrobat (PDF) 16kB Jan31 10) from Florida State University.
Another example is to delete a certain number or percentage of questions. You could delete 33% of the questions then assign the clicker portion based upon the points earned from the remaining 67%.
There are two main objectives with a forgiveness policy. First, the student is assured that technical failure or minimal forgetfullness will not harm their grade. Second, no extra work is required for the instructor. Creating makeup clicker questions would be a nightmare!