They are if you're using quality fillers. The trick is to use it sparingly first of all, and to make sure you prime any areas you plan on filling. If the wood is soft and mushy, forget it. It needs replaced. Don't caulk gaps larger than 1/4". Anything larger needs a backer, and I'd recommend vulcum for those areas. I use 1100A siliconized latex from SW that has a 55 year warranty. For wood fillers, there are many choices...the important part is that you prime, fill, and prime again. If you don't protect the filler or the filled areas, and give it something to stick to it will fail. Also, filling nail holes is a whole different story from filling large holes on rotten wood.

If you're talking rotten wood though, you really should replace it, find the source of the rot and remedy it while the wood is removed. Back prime anything you replace by priming the entire piece of wood, front-back-end grain.

Hope that helps.

 

Definitely not rotten. Fresh boards, primed and painted twice on all 6 sides. Nailed them up around the window, and due to the shape of vinyl windows, and minor imperfections, they don't fit snugly against the edge of the window.

 

Oh, that's typical. Just caulk using a quality siliconized latex. If the gap is over 1/4" cut a slice of backer rod to fit and then caulk. Any quality wood filler or exterior spackle will work fine for the nail holes.