D&D 3E/3.5 Spacing and creatures in D&D 3.5

[eamon]

No you haven't missed anything. Just use the squeezing rules, perhaps slicing up the squares into 2½ft x 5ft rectangles so you know where everyone is. If you don't mind added calculations, have people with ranks in profession (sailor) make a check vs. DC 15 every round (beginning of turn) to negate half the squeezing penalty, maybe DC 25 for the whole penalty.

Also, don't forget to consider things like, maybe, balance checks.

These are good ideas. Sometimes you just can't avoid stuffing multiple creatures into a 5 foot square, so instead of demanding that half of the players remain prone or jump out of the boat, an ad-hoc solution is required. You might allow sneak attack against the creatures thus disadvantaged.