If it rains hard enough to affect the game, it would be called or shortened anyway, and if it's not raining hard enough to affect the game, then it's a moot point.
Most people seem to say it favors the over, gets the starting pitchers out of rhythm if there is a delay, bullpen probably has to pitch more innings, not much traction in the field for the fielders, blah blah blah... But I have been tracking a specific weather related totals angle this season in MLB, and my data says otherwise. Even though the sample size is fairly small, it is drastic enough to where I can definitely say it favors the under. I wouldn't blindly take the under in every game there is supposed to be rain, but if the under makes sense from every other angle, rain should only help.
Pete, like 70KGman said it is a very small sample size. It doesn't mean that long term its +ev to hit the unders. Just by the parameters being used I guarantee that its not of statistical significance. Good luck on your bets though.
Rain causes balls not to fly as far (usually cooler temps), but at the same time cause fielders to not be as fast. I think totals are higher in the hot sun due to the humidity causing balls to carry...
Rain doesn't affect baseball totals since the game is suspended when it rains. Rain only affects football and soccer totals and that is if it rains extremely hard and the pitch doesn't have an underground drainage system.