The most challenging smell is the holding tank and this is typically from the hoses - change them.  Diesel fades quickly, need to find the leak.

once these are fixed and give the boat a good airing.  Put the cushions out in the sun and air.

To solve this same problem, which I had when I bought the boat, I installed a portable floor air conditioner (from Home Depot) in the aft cabin.  I strapped it to the starboard bunk with simple ratcheting straps.  I ran the exhaust hose so  that the hot air exhausts out through the rectangular porthole in the aft by the helm station. 

I used only duct tape and bungee cords to hold the exhaust hose against the porthole, since I did not want to cut any holes in the boat or permanently change it.  
 
This keeps the boat actively ventilated and dehumidified as well, which keeps the mold at bay. It pulls the fresh air in through the cracks in the main hatch.

It also becomes a minimalist air conditioner in the summer, dropping the internal temperature a few degrees, allowing me to survive the hottest Miami summer days on the boat if I sit right in front of the a/c.

The women in the family, who seem to have more sensitive noses than the men, say that the boat always smells nice...but I watch their noses closely for any twitching movement in case they are just being "nice".  :-)

Seriously, this was an inexpensive solution which has worked well for me for 8 years now.

The only downside is that I lost the starboard bunk, but for long cruises the a/c can be easily removed to gain the bunk back.
 

Peggy's book is great for odors.  She is also helpful on Sailboatowner.com

http://shop.sailboatowners.com/prod.php?53615

Les
 

Marc & Susan;
Tracking an odor on a boat can be tricky business. Certainly try all of the foregoing. But here are my Suggestions; First, find that diesel leak from your engine. Check the fuel return and input lines for the tightness of the hose clamps.If you can find a way to conveniently wash the oils off the engine, then do that too - and of course, put a clean diaper under the engine and change it frequently.
The the dead space storage areas are prime places for mold to grow in an older boat; i.e. behind the seat cushions, under theV berth, etc. First, wash those areas with a mid solution of bleach and water (or Tilex) then paint those areas and the bilge with some thing like Interlux Bilge paint. About 1 qt. should do it. A bit time consuming but well worth the effort.
Third; try using a few drops of eucalyptus oil in the bilge to sweeten the smell.Usually available at a heath food store. On a temporary basis, that will sweeten the overall odor.
If you have access to 110 Volts AC, use a fan to keep the air moving about the boat during down time.

Marc,
Based on your description it would appear that the musty smell is the most prevalent problem. I'm including  a link that discusses how to remove musty odors. http://www.ehow.com/how_5301033_remove-musty-odors.html?ref=Track2&utm_s...

Although the discussion is more about a home and the need to control moisture I think it might give some insight for the boat owner. I believe you need to address moisture in some areas which you really can't see i.e. under the forward cabin sole there is a portion of the bilge that does not drain. You also have the section in the forward cabin under the drawers that accumulate moisture. If you check under your galley under the sink this is another spot that can stay damp and if an older boat these have been in the works for some time. You may need to get into it.Almost every fall and spring I have taken straight bleach and spray all the areas and let the bleach stand as it will work and clean any mold. You should spray and step outside, let it work.
You will note in the link there is a section on removing the odor from wood and to my surprise we have wiped all the wood surfaces over the years with a mild bleach and water solution prior to re-oiling the teak. In the head I pretty much sealed all wood with Cetol finish so moisture does not soak into the wood.
I noticed this website discusses some tea oil or citrus oil and I'm thinking there may be some merit to trying that on the upholstery and when sitting still on a sunny day bring a cushion or two outside and let them sit in the sun. a few hours as suggested.
Ventilation I have a solar powered vent mounted into the  hatch in the head and with the dorades and this vent they move the air through the boat. I put a hook at the top of the head door just to keep it open a couple of inches when we are not on the boat.
As to the diesel odor which seems to be your next problem by description, I believe if you do like others suggest look for loose clamps etc. and try to find the possible source. One thing I noticed that was not mentioned is that your fuel tank may itself be leaking through small pinhole or pinholes on the bottom of your tank. My boat older than yours had this problem and I replaced the tank as over the years the bottom had developed corrosion and thus the slight seepage.As to the odor of diesel a oil burner technician friend of mine  says white vinegar can  reduce the odor.
For the most part after 13 years living with our boat we don't seem to notice any strong odors when arriving at the boat.
 

I've cleaned up a couple of 25+ year old boats, turning stinky/mouldy to squeaky clean/fresh and it is a physical problem, not a mystery, per se. 

Step 1:  Remove all the cushions and cubby area covers and drawers from the area you are going to work on, like the V-berth.
Step 2: Feel around in every single cubby and crevice that feeds into the bilge and, using an electric drill  with a half inch bit and a GREAT DEAL OF CARE to not drill through the hull, drill holes from the lowest point of each cavity so that any water in them can drain out into the bilge.  A set of those conical and round file bits is helpful to expand the holes.  Don't worry about cleaning up the dust.... (The hole from the V-berth must be made dead center under the drawers frame.)
Step 3:  Ensure that your bilge pump is 100% functional.
Step 4: Buy or borrow a small (lower pressure) pressure washer that has a suction hose for adding soap to the stream and buy a big bottle of cheap bleach.  Bring a water hose and the pressure washer into cockpit, or onto the deck and put the hose down through a hatch, hook everything up and, using the pressure washer wand to get up into ever space between the liner and the hull, as well as every single surface of fiberglass or wood USING A WIDE TIP SETTING (minimize any wood grain damage).  Blast every surface including the underside of the fiberglass beds/seats and make sure that the black mould is coming off the fiberglass surfaces and the white mould is coming off the teak.  Check to make sure the bilge pump isn't getting clogged.  Work your way from side to side and front to back of the vessel.  You might do a second pass using a big bottle of detergent instead of bleach, but usually the bleach does the job alone.
Step 5:  Use fans to dry all areas out thoroughly BEFORE putting things back. 
Step 6: Per the advice above, trace every possible leak from the fuel lines and tank and engine.  If you don't find that source the diesel smell will never go away. 
Step 7: Use a degreaser foam spray on the engine and rinse it off, using a toilet brush and a toothbrush to get into the crevices.  Do the same to the inside of the engine cover, but you won't require the bleach or pressure washer -- but prepare for lots of splashing in and around the galley. 
Step 8:  Same thing goes for under the aft bunks, cabinets and around the water tanks. Under the galley sinks, remove the teak box under the stove with the 6 screws there and spray in there, too.  Same thing with the cubby behind the toilet, etc.  Try to get back in from the top of the fuel tank to spray up and under the engine and the navigator station.  A gutter cleaning "J" type attachment can help.

If you do this thoroughly, you will have cleaned the inside of the hull below the waterline where the biggest build up of condensation and black mould gradually builds up, as well as rinsing out a lot of engine debris. 

I ended up replacing all the nasty old hoses on one 1978 vintage boat, but on the 1991 C 36 none of the hoses look like they need replacing, but many of the stainless hose clamps were loose and could have leaked odours, so check them all.  This has kept the boats smelling great for years, although some work on the fuel tank has meant it needed some soap and hosing down again. 

Best of luck, Kevin

Changing the 5/8" vent hose to a proper sanitation hose (Shields Series 148) was the ticket to rid the last of my smells aboard. I was surprised the vent was the cause, but changed it after wiping all the others (that are not original), flushing the system, rebuilding the head and not determining the source. Kinda makes sense in that the original hose was 16 yr old common water hose. Gotta love rare a $30- fix :) I did and do flush with fresh water from the sink as well

We have some odor issues on our boat that I have never figured out.  Everything is fine until we have to close the boat up and run the air.  That seems to bring all the odors to a peak.  We have started using TeaTree oil in the air return and that seems to help.  We have changed all waste hoses (except the vent line from the tank- thanks for that reminder). We do use a Hepa fan that runs 100% of the time we are not on the boat and that helps keep things dried out and fresher too.  This year I rerouted the Diesel Blowby tube that just dumped into the bilge to an oil separator and back to the air intake on the engine.  I think that has been the best odor elimination for me so far. But I'm still working on it.
 

I did the same with the blow by line and was one of the best thing to clean up the smells 

Our boat is totally order free after chasing odors for a few years.
Here are the big things that help us;
1. We fully cleaned with Tilex and then painted every covered up area we could get to using Interlux Bilge paint. Removed the draw sets , panels, water heater, painted the entire bilge area and any other we could get to. Then, using an oil based paint, painted all of the boards under the seats.
2. Scrubbed down the engine.
3. Aired out the cushions
4. Did the interior teak with Liquid Gold furniture cleaner.
5. Always used fresh water in the head.
6. We keep a fan and de-humidifier in the boat during the off season.
The boat is completely free of odors and is a real pleasure.

Great ideas.  Before closing up the boat for winter we bring a ten pound bag of charcoal, cut length wise and open slightly.  Will help to absorb musty odors.
Put fabric softener sheet in all drawers.  Empty bilge.  Wipe down bilge areas with Lysol wipes.  Find that diesel drip!  If possible leave a small fan circulating air when boat is closed.  Replace holding tank hoses - make sure to buy the right type of hoses.  We also subscribe to the practice of “if its brown, do it in town” (if it’s gonna be brown, use the yacht club or marina facility toilet).  Use fresh water to flush the toilet into holding tank.

The wonderful age-old battle against boat odors where you can win a battle, but never the war.  What I have learned with my boat is the holding tank odor is the worst one.  I replaced all of the hoses with good quality ones (don’t forget the vent hose as this is normally the worst for odor) and the holding tank.  Never let a vendor tell you that the holding tank can’t become permeated.  I replaced mine and you can tell when entering the boat. 
 
The other common smell is mold and keeping everything clean is helpful on that front.  I have in-mast furling and the rain water that comes in leads to an issue with mold at the base of the mast. So regular cleaning of the base is normal on my boat.
 
Lastly I made a vent fan for the small hatch in the galley that I leave on a timer so it runs for several hours during the day.  That is a great way to bring fresh air in while off the boat.