Let me guess, your valleys are done in the "closed valley" fashion like so many homes these days are. Funny you should bring this up because a buddy of mine is a roofer and we were having this very discussion. The weather here in Wisconsin gets very severe. here is what we do (and roofers up here all suggest this).
1) Put "Ice and Water" material along bottom edge of all roof area. Put it overlapped 3 feet up from the ridge on the bare wood.
2) Use "W" flashing in the valleys. You can't beat it's protection from rain.