"we need help in order to get them through the winter."

Generally, trees get through the winter on their own. What, specifically, are you considering here? If they are in such bad shape that they won't make it thought the winter without intervention, they should probably be removed/replaced.

"We don't know what to do to help them or even fertilize them for fall."

Don't over-love your trees. That will often kill them quicker than anything. If there is a reason to think they need extra nutrients (signs of nutrient deficiency), then carefully applying the necessary fertilizer may be beneficial. If not, then DON'T!

"Some of the bushes seem to have some type of fungus..."

Without pictures or detailed information, it's hard to know how to advise you on that. It isn't by any chance lichen is it? If so, lichen is completely harmless to your plants, although it may be a sign that the plant is less vigorous.

"... some of the trees have a lot of dead limbs and dying leaves."

Here again, it's hard to know what's going on without more info. Even healthy, mature trees have dead limbs, but atypical amounts of dead limbs could be caused by many different things. Knowing the type of plant, having detailed pictures of both the entire plant (enough to see damage pattern) and of specific damage (for possible disease/pest diagnosis), and other relevant information might be helpful in figuring out what's going on.

"Does the extension service have people available to come and look and advise?"

In some cases, yes, but you should call and ask. Often they won't come out except in specific cases (and that may vary by location).

"How about the master gardeners?"

Expertise of master gardeners varies greatly, but they generally would not be my primary source of information in cases like this. Often, their training is very limited.

An ISA-certified arborist would probably be a reliable source of information, but, they are probably going to charge you for anything much more than a quick sales pitch for their services.