Time could very well be the most pervasive theme, one that runs throughout all of the sonnets. In order to consider such a broad topic, you should understand that, by most scholars, the sonnets are considered to fall into two groups.
There sonnets are considered to be addressed to a "young friend," and, as relates to time, are encouraging this friend to marry so that his beauty may carry on in his children. And there are sonnets considered to be addressed to a "dark lady," a mysterious figure that the poet appears to love, but have mixed feelings about as well.
Time is used throughout the sonnets as an enemy to be defeated, and one way the poet determines to defeat time is through writing and leaving a written legacy behind. In essence, he may not live forever, but his words shall.
Beauty is seen as related to time, in that it fades with age. The poet does take on this theme throughout the sonnets, but again, his consideration of...
beauty is different with the different persons he is addressing. When he addresses the "young friend," he does extol his beauty, but doesn't really ever describe it in detail. With the poems written to the "dark lady," he spends much language on description of her beauty -- language that is often times satirical and disdainful.
Time and Beauty are important themes in the sonnets, their uses often bearing direct relationship to whom the poet is addressing the specific sonnet.