The clear choice for me would be a Fusion IP-500 head unit.
Its IP65 rated (far more 'marine' than anything else out there), has an internal iPod dock (so you flip the front down, put your iPod inside and forget about it). Multi zone control (so you can independently control the volume on the tower speakers and in boat speakers, even the bow speakers too if you want.
It has a stack of cool EQ style features such as adjustable high pass, low pass, cross over's etc etc... Its easily the most advanced unit I've seen when it comes to marine stuff.
The sounds not half bad either ;)
Link -
http://www.fusioncaraudio.com/north-and-south-america/marine-audio-2/stereo-units-15/msip500-56-product.aspx
Hybrid Mode
