UPDATE tobeupdated
INNER JOIN original ON (tobeupdated.value = original.value)
SET tobeupdated.id = original.id
That should do it, and really its doing exactly what yours is. However, I prefer 'JOIN' syntax for joins rather than multiple 'WHERE' conditions, I think its easier to read
As for running slow, how large are the tables? You should have indexes on tobeupdated.value and original.value
EDIT: we can also simplify the query
UPDATE tobeupdated
INNER JOIN original USING (value)
SET tobeupdated.id = original.id
USING is shorthand when both tables of a join have an identical named key such as id. ie an equi-join - http://en.wikipedia.org/wiki/Join_(SQL)#Equi-join