This may be heresy to some, but San Juan Worms and other worm patterns.

A former Southwest Wisconsin guide once gave me this advice, "Generations of Wisconsin farm boys have fished worms after it rains. So should you."

I'd think the advice still holds when it's raining.

If the water gets to look like coffee with cream, the biggest nymph you can cast might be the way to go. Or swing a muddler-type streamer with a big head that pushes water.