Ideally, you should acknowledge every present immediately, but sending it within two weeks is also acceptable. The period surrounding your wedding is a busy time; if you fall behind, make every effort to send a thank you as soon as you can -- but no later than three months after the event.
To ensure the task doesn't become too overwhelming, write notes in small batches. Diane Warner, author of "Contemporary Guide to Wedding Etiquette" (Career Press; 2005), offers this strategy: "Set a goal of writing three or four thank-you notes per day. Don't try to tackle them all at once, otherwise they may tend to start sounding trite." She also recommends that both the bride and the groom divide the note-writing duties.