what kind of effect will all the rain we've gotten in Eastern NE   have on the Bass? and what is everybody using now that the water on most of the lakes has gone from what somewhat clear to muddy?

We did some fishing at the Valentine Refuge lakes in north-central NE over the weekend.  We were out in the nasty rain and wind, and figured that with the raised water level and tough conditions the bass would be holding very close to the shore, but we were catching them left and right at the edge of the rushes at least 100 feet from the bank.  Our best luck was with brown plastic craws. 

I'd say your best bet would be to work as close to the banks as you can, but if you have cover that extends out into the lake you'll probably find bass there too.  Just my 2c.