Origin and meaning of "every cloud has a silver lining"
Solution 1:
According to The Oxford Dictionary of Proverbs, the phrase "Every cloud has a silver lining" is
a poetic sentiment that even the gloomiest outlook contains some hopeful or consoling aspect. Cf. [1634 Milton Comus I. 93] Was I deceiv'd, or did a sable cloud Turn forth her silver lining on the night?
Read more: http://www.answers.com/topic/silver-lining#ixzz1Cu5fvfWP and http://www.etymonline.com/index.php?search=silver+lining&searchmode=none
Both cite John Milton's Comus 1 as the first instance of this expression.
Solution 2:
The idea of clouds having silver linings comes from the fact that when the sun (or moon) bursts through a cloud it looks as if the interior is silver.
The sun bursting through a cloud is a good metaphor for a problem eventually having a positive outcome.