Here's an article on how to make your own home brew rot killer.
If you have an area that's rotting out and that will be expensive to replace there's a good chance you can restore it using a penetrating liquid epoxy. It soaks into and hardens the rotted wood. If chunks are missing there's a putty-like epoxy patching compound you can use to fill these areas. This stuff isn't cheap, and the process is tedious, but if the alternative is a lot of pain or big bucks well . . .
You can read about it at the Rot Doctor. If you believe the doctor's PR he's got the best of this sort of product, but you can buy a similar kind of stuff at boat stores and some home centers. One brand name is Liquid Wood, another is GitRot, and yet another is called West Systems (boat people use the last two).
Scrape/trim away any wood that crumbles easily or is falling out. Don't get carried away with this, the liquid epoxy will soak into areas that have reasonable body left and make it solid again. Let the area dry out (cover with plastic when rain is expected).
Drill a honeycomb pattern of 3/16" holes to help the epoxy penetrate throughout the decayed area. Drilling at an angle helps, particularly on vertical areas, Note: You want the liquid to puddle in the holes, so don't drill all the way through.
Use the putty like epoxy to fill the missing areas. The stuff hardens quickly so don't make up larger batches than you can get into place rapidly. Let cure and smooth the surface. I've never used the epoxy putty for this, so I don't know whether you should try to shape it before or after it's completely cured.
Experiment with the stuff on scrap wood before doing the real thing
A cheap and widely available alternative for filling the missing areas is a car body repair filler called Bondo. You can get it a auto parts dealers.
I also use Durham's Rock Hard water putty for the filler. Maybe just because I've used it so much, but I find it easy to use. It's a powder you mix with water. It doesn't shrink, and as the name says -- it dries hard. You can sand it smooth after it hardens. The repair mustn't be exposed to moisture however -- it's gypsum and will absorb water and swell. So, it's best for indoor repairs, but when exposed areas are well coated with paint, I haven't had a problem. It's cheap and keeps forever. My repair shelf is never without a can of this stuff.