While the ゐ and ゑ characters were indeed eliminated from common use, there never was a WU character, at least not officially. The wikipedia page linked by Amanda mentions attempts to create a proper equivalent to the other わ行 letters just for the sake of completeness, but this letter (which looked like 于 in katakana but apparently had no hiragana equivalent) had never seen wide use.
The reason for that is that the sounds /wi/ and /we/ were indeed in existence in Japanese at some point of time, so they were naturally given their own letters - but there has never been any /wu/ sound (as well as any /yi/ sound) in Japanese, and thus it wasn't given any letter.
That's not to say such sounds are impossible: English has both sounds (/wu/ in would, /yi/ in year, which most Japanese speakers would pronounce the same as ear). It's just that Japanese never had them. /ye/ is a slightly different story: Japanese does have a distinct /ye/ sound now (written as イェ, though some people may pronounce it the same as イエ). And it also had a /ye/ sound back in the Edo period, but it was actually just the normal pronunciation of /e/ in the beginning of a word (which reverted back to /e/ in modern times). That's where some English spellings such as Yen, Yebisu and Yedo come from.