uuencode is a format for encoding binary data.
FPX The uuencoding format has a troubled history. There is no formal specification for uuencoding, and while it was a de-facto standard throughout the 90's, implementations have varied wildly in realizing some of the format's subtleties. This includes variations in line lengths, extra "parity" characters at the end of each line, and the encoding of '0' as either the space character (in which case spaces at the end of a line may be truncated) or the tilde. It gets worse when you consider possibilities for splitting uuencoded files across multiple messages. Using a "fair-weather" package like uudecode may have a suboptimal success rate for decoding real-life messages, when used without preprocessing. (Shameless plug: uudeview was written to handle many of the more terminal cases.)
These days, the use of uuencoding is decreasing. In E-Mail messages, it has been almost fully replaced by MIME. It remains in lesser, but still active use in newsgroup, along with MIME and yencode (which has its own share of problems, not unlike uuencoding). New software should refrain from using uuencoding but for legacy purposes.
See also uudecode