I use a two part filler (like car body filler) that comes in a large variety of wood shades. It is not exactly flexible though - is there such a thing? It has quite strong bonding properties though, so if the wood isn't moving too much the cracks don't tend to re-open. With larger cracks and holes it will always show to some extent after a few months outside.
Is the wood to be painted? If so use external frame sealant (it's like silicone/mastic, but can be painted). Very good filling properties for quite large cracks and remains flexible forever.
Thanx Noel, had many fun times trying to paint over silicone sealant, got around it though by painting it first with exterior smooth emulsion then undercoat then gloss, amazingly it didn't flake and is still good today three years later, however, I won't make the mistake of using silicone again if anything needs to be painted afterwards :wink:
Apologises for contradicting you Noel, but decorator's caulk isn't suitable for external use. It goes on fine and can be painted, but it just doesn't hold up to weathering. The best product is called "Exterior frame sealant" -it is not silicone based. Can be bought anywhere like Wickes etc.