well, i unfortunately drove through a puddle tonight, which came out of nowhere due to poor visibility in the downpour. anyways, my car continued to run, but my check engine
light came on and the car/engine was shaking and vibrating pretty badly when i stopped at lights. engine power was reduced dramatically at lower gears, but after hitting about 25mph, it didn't seem as bad in terms of engine shaking. i was able to drive home, which was about 3 miles.

 

you got water in the electrical system somewhere, clean and/or replace....
cap, rotor, plug wires. reset ecu when done

 

How deep was the puddle do you have a CAI? I've never actually seen a case of it, but if you submerge your intake in the puddle you can end up sucking up some water and cause hydrolock. Now on the lighter side if the filter just got soaking wet it could be choking trying to pass air through it. Also look at racerx suggestions.