[NCountry]

Speakers - just an fyi - you can hook 8 ohm speakers to a 4 ohm receiver. Don't hook 4 ohm speakers to an 8 ohm receiver. 2 8 ohm speakers hooked to one side of a deck will make a 4 ohm load so you can hook two 8 ohm speakers per side IF the receiver is rated at 4 ohms.
IPOD's - The small speakers that plug into the headphone jack on an IPOD do not produce sufficient sound to compete with the noise level of a boat under sail. IMHO they are a waste of money. There are several small docking stations on the market now that will work nicely if you aren't to concerned about sound quality.
The advice about different charging options is right on. There are also now several "kits" you can buy that may cover most of the charging options.
FM Transmitters - work great if you set the IPOD and transmitter right next to the stereo. However, these little units are not very robust. We've tried multiple brands and they always go down within about a year. They are, however, a great option for something like a charter as long as there's an FM receiver onboard AND you're not in an area with a lot of FM radio stations. Take along lots of extra batteries for the transmitter. They tend to lose range and sound quality as the batteries are drained.
JUST a small bit of info - after multiple tries to get music from our IPOD to the boats sound system we recently put a new stereo onboard. It has a USB connector for the IPOD so you can charge it AND listen to the music on it. This has turned out to be the ultimate great way to take our music with us.
SUBWOOFERS - bass is very omnidirectional so a subwoofer can be placed almost anywhere as long as there is some sort of a port for the enclosure it is contained in. If you have the room and the door has a vent or port I might suggest your nav station or on a bookshelf as a great option. Also in the galley somewhere that has a vent or port as long as it doesn't disturb the galley wench.
Know that's a lot of info but thought this was a good place to post it.