Like so many things, "it depends". A weekend trip in anticipated warm, dry, sunny weather will require a different packing strategy than a 3-week trip with a lot of stream crossings and anticipated multiple days of rain. When my wife and I hiked in the narrows in Zion National Park (walking through water, at times waist deep), we were glad to have a pack-sized drybag to put pretty much everything in.

I'm like Glenn in that I typically use a poncho, but as I live in the Pacific NW, I typically use a trash bag whole-pack liner too. I do use the factory stuff sack for my down bag, as I don't want to compress the down any more than that. For a bulkier synthetic bag, I'd use a compression sack if I had to (to fit everything in), but would rather use a down bag ...
I put the stuffed bag in a plastic bag just to be safe.

Apart from keeping gear dry, stuff sacks are about organization --- so different colors help. Plus perhaps you might want an odor proof bag for food (and other smellables).

Since as has already been stated, normal stuff sacks aren't waterproof, IMO there's no reason to get a standard ~heavy nylon stuff sack. One can by "ultra light" stuff sacks of silnylon or the like for not too much money. For times when you really want to keep things dry, then some sort of plastic sack or even ziplock bag can help a lot.