I use ziplocks for nuts, fruit, crackers, cookies, chocolate. Clif bars et al, as you said, are fine in their own wrapping. These things will keep for many weeks without vacuum packing.
For oily stuff that can spoil and/or leak grease - cheese and meat (salami, jerky, smoked fish) - I vacuum pack and leave it vacuum packed throughout the hike. I wrap each meal's portion of cheese & meat in saran wrap. Then, four meals worth get carefully consolidated, like puzzle pieces, in each vacuum bag. Every other dinner I open a new bag to expose meat & cheese for two dinners and two lunches. That way, I only have 6 vacuum bags for a 12 day hike. The vacuum bags do take up a bit more room than ziplocks, but it keeps that oily stuff from leaking and it increases its shelf-life.
And one hint, in case you didn't think of it... The butcher at my local grocery store is the one who suggested this approach, when I asked his advice about which kinds of meat to take backpacking. And the butcher does the vacuum packing for me. He gives me bags, I stuff them at home, and bring them back for him to seal. The first time I did this I didn't ask him to put the seal as low on the bag as possible, and I ended up with 2-3" flaps of plastic which I couldn't cut off. That did make it harder to consolidate the bags in my pack. Since then, I ask him to put the seam as low as possible, and it's been great.
Hope you enjoy your JMT hike! Amy