Yeah, last time it rained here in Austin (about 4 months ago), I ended up with flooded floorboards in the front. Turns out the sunroof drainholes were clogged. I simply cut a long piece (about 4 feet) of weedeater line and fed it through.
I poured a glass of water down the lines and they drained right out to the garage floor. If it ever rains here again, I'll see how those snaked-out holes hold up to a real rainstorm.