Our top suggestions for odor control:
- buy $10 cheap clip on fans from hardware store.  When we leave boat, leave one fan on in aft cabin, one fan in front cabin with doors exiting bathroom. 
- suck out bulge water, (we use a “water blaster” toy water cannon made out of PVC type tubing.
- add 2-3 cups vinegar and paint the bilge with vinegar (or mild bleach water solution).  Idea is to kill off bacteria that might be growing in bilge.  If you use bleach solution, thoroughly flush out bilge well with fresh water (bleach is hard on gaskets & pumps.
- Always suck out bilge as much as possible before leaving for more than a few days.  Dump in 1-2 cups vinegar in bilge, no need to flush out.  
- use desiccant bags such as DAMP RID.
- never poop in toilet (“if it’s brown do it in town”)
- only use fresh water to rinse toilet, not lake or river water.

More tips to eliminate odours:

1. Good tips from Peter Gutierrez!  I now suspect I may have done in two Whale SuperSubs by leaving bleach in the bilge...
2. Try the new "Eva-Dry" 'rechargeable' drying units. We got ours at Costco but the chandleries are starting to carry them.  Orange when dry, green when wet, plug in to 110 volt to dry the crystals out again.  We use one in each hanging locker.
3. Make sure your Dorade style cowl vents are open.  You must screw the control knobs CLOCKWISE all the way to open them and they should point in OPPOSITE directions to vent properly (one scoops air in while the opposing one sucks it out due to the vacuum effect of wind passing around it -- most people leave both facing forward and reduce the volume of air flow significantly).  If you have them set this way, you have no need of solar powered fan-vents.
4. Use a bleach spray once a year in every nook and cranny under and behind all the drawers, doors, floorboards and cubbys to eliminate the black mould.  After drilling (not through the hull!) out drainage holes from every cubby to the bilge, I actually bring a hose inside and spray everywhere after the bleahing, then leave things open for a warm, sunny day or two to dry out.
5. I similarly shampoo the engine with degreaser once a year and spray it off and spray aft under the sink.  Gives the bilge pump a workout. 
6. Use Concrobium's Moldex (or similar) in an aerosol to get up under and behinde all the liner panels throughout the boat to help prevent black, white and red moulds from forming. They sell it in an aerosol can for fogging in tight spaces.
7. Consider buying a cheap, small sized wet-dry vac to suck ALL the water out before leaving the boat.  I use a BridgeNorth "Boat Hook Bailer" hand pump, but the dollar store water gun idea is great!
8. If you don't have the fridge drain going through the foot pump to the galley thru-hull, make sure the hose reaches all the way to the bilge to avoid water spreading everywhere.
9. I'm adding a drip tray with a drainage tube leading back to the bilge under the prop shaft packing ring to further reduce the constant stream of water running under the floor boards.  6" paint roller tray with 1/4" plastic tube and the appropriate fittings through the hole I drilled to make the set up watertight.
10. Check all your water fittings for leaks.  I have found a few drips over the years.
11. BUY A BIG ORANGE waste tank vent hose filter and enough sanitation grade white hose to add a loop that goes up from the lower cubby up and back down the cubby behind the settee cushions aft of the port chainplate.  Just needs a new bag of charcoal once a year and does an amazing job of eliminating the odour.
12. Also check/tighten all the hoses on the waste tank and vent for leaks.  I replaced the odour-saturated original vent hose with sanitation grade white hose.  The original standard reinforced clear hose eventually gets stinky.  When it's brown, I now just flush it down!  No noticeable odours.