OK, here is my pre-treatment method. This is just one step in a five-step procedure for painting and glazing sash. This is not the only way to deal with pre-treatments. Please post yours.
Source: Save America's Windows, page 182, and Historic HomeWorks Forum, http://historichomeworks.com/forum/viewtopic.php?p=2466
This procedure assumes the double-hung sash are new and unprimed bare wood, or have had all paint and putty removed down to bare wood, and that all woodwork repairs have been done.
Do not apply any treatments, primer or paint to the side edges of the sash. Leave the edges bare wood, which leaves a surface where the wood of the sash can dry out, preventing peeling paint and keeping the wood free of fungal decay.
A pre-treatment may not be necessary if all the wood is perfectly sound (as with all new wood) and a very effective primer is used, but I find I can lengthen the service life of the paint coatings on old wood with this "fine tuning" of the coating system. Scientific studies at the Forest Products Laboratory have clearly demonstrated that a paintable water repellent preservative effectively adds to the protection of the wood and dramatically limits fungal decay extending the window's life.
In many cases the exposed surfaces of the sash are weathered and need a pre-treatment, while the glazing rabbet is perfectly sound wood and needs no treatment because it has been protected from the weather by the putty and glass. In fact, a pre-treatment in the rabbet may prevent good adhesion of the putty because the oil of the putty cannot seep slightly into the surface of the rabbet. This must be balanced with the fact that too much oil can seep out of the putty, leaving the putty weak right along the surface of the rabbet, leading to putty adhesion failure. The proper balance is found in the worker who can judge the character of the wood and the putty to create a successful and long-lasting seal between the wood and the glass.
One of the traditional practices is to always pre-treat the glazing rabbet with linseed oil, or a linseed oil and turpentine mixture. This still works, but some scientific studies have demonstrated that linseed oil acts like food for the mold and bugs that damage paint and wood. A recent practice to avoid this is to use other materials to seal the glazing rabbet, such as alkyd-resin oils and primers, that are less like food to the mold and bugs.
If needed, apply a penetrating pre-treatment to the bare wood. Apply the pre-treatment to both faces of the sash, all muntin bars and muntins, possibly including the glazing dadoes. The bottom edge of the lower sashes' bottom rail may need treatment if it shows signs of deterioration caused by water; if the bottom edge is in good condition it should not be treated since it has done well for so many years without treatment. Do not apply pre-treatment to the side edges of double hung sashes, and the top edge of the upper sash.
There are two types pre-treatment, 1. Paintable water-repellent preservative, 2. consolidating oil-resin. Paintable water-repellent is suitable for sound wood surfaces. (if waxy paraffin type (Forest Products Lab's WRP Recipe, Thompson's WaterSeal, or similar) apply to all surfaces of the sash, if sticky oil or resin type do not apply to sash edges (the surfaces that run in the jamb's sash tracks) and face margins (the narrow strip where the face of the sash rubs on the parting bead or the stops) Consolidating oil-resin treatment is suitable for gray weathered wood surfaces or surfaces that are somewhat "soft" or more porous than perfectly sound wood. The traditional recipe for this treatment is linseed oil and turpentine. I no longer use linseed oil because it is susceptible to mold and fungus attack. I now use a 50%-50% mix of mineral spirits and oil-based alkyd-resin varnish or a proprietary product (Flood's Penetrol, or similar) Just to confuse us all, there are some combination products that may be suitable. (California's Storm Stain Penetrating Wood Stabilizer, or similar) Water-based products of both types MAY be suitable, but all my experience and this recommendation is for oil-based products.
Penetrol is an oil-based product made of mineral spirits, linseed oil and alkyd resin that penetrates deeply into the wood surface. The mineral spirits evaporate leaving behind the oil and resin that cures and consolidates loose fibers at, and just beneath, the wood surface. Apply putty or paint primer when the pre-treatment is 80% cured. The amount of cure time is dependent on weather or shop conditions. Penetrol is like a light varnish or like an alkyd-resin oil-based paint without the pigment.
Storm Stain is a waterborne product that contains zinc napthanate and a very tiny amount of resins. Zinc napthanate is a preservative that limits mold, mildew and fungus. The resins help hold the zinc napthanate in the wood, but there is not enough resin to consolidate loose fibers at the surface of the wood. Storm Stain does not penetrate as deeply as oil-based pre-treatments because it is waterborne. After 24-48 hours the water has evaporated, the wood surface is dry, slightly tacky to the touch and ready for paint primer.