The best rain effect I've seen in a comic is the one used in 'Purgatory Tower' on the latest strip:
http://www.drunkduck.com/Purgatory_Tower/
See how Silent Kitty emphasises the water ON the people and objects, dripping off them, and the mist of the water drops scattering when they hit surfaces, then puts a small amount of mist into the air, and just barely some little hints of actual raindrops? I think that's the direction to take things in. Lots of transparent layers and using grey and white rather than blue.
Aw, thanks Darth! If you have Photoshop, the rain drop effect is super easy:
1) Take mouse, small brush, and white color. Make dots all over your page. Hundreds of dots! (If you're not as OCD as me, you can also make a few dots then copy and paste them all over the page.) Vary your dot sizes so that some look like they're further back, and some look closer to the "camera". The majority of your dots should be small. Now it should look like your characters are caught in a horrible blizzard.
2) Filters --> Motion blur. Change the angle that your blur is at, depending on which direction your wind is blowing in. On the page that Darth linked to, there's no wind, so the rain is falling straight down. Make sure you make the effect long enough (I usually set my "distance" at about 90 pixels) so that your raindrops don't look like tiny white worms falling from the sky. Ew!
--> 2b) If your rain is not falling straight down, you should make 2-3 layers of raindrops and vary your angle juuuust a little bit on each one. Next time it's raining (and wind..ing), look out your window. When the wind blows, not all of the drops move at once, so you get a cool effect where the drops farthest from you look like they're moving faster than the ones close to you.
3) Make a new layer on top of your ink, get a transparent brush and turn the opacity way down. Decide what areas the rain would be hitting the hardest (on top of people's heads, on their shoulders, on objects surrounding them) and just run your brush over that area a few times so that it looks "misty". Turn your opacity up, and put a few white dots in the mist so that it looks like the rain is splashing.
4) Make thin trails of white or light blue ( these are your "water trails" ) run out of the misty area and make sure they follow the contours of what they're running down! If you're not sure how they would move, stand in the shower (or even better, in the rain) and pay attention to how the water acts when it hits you.