One, although the OCT is not a wilderness trail, unless you have some experience backpacking (and possess the skills and spirit of self-reliance that implies), I recommend sticking with day hiking. There are many challenges involved, including timing of the tides, uncertain campsites, sometimes very long distances, etc.
Two, where you go is dictated somewhat by what kind of shape you're in and how far you can or are willing to hike in a day. Distances between developed or even rough but legal camping spots (or even motels) are far on parts of the Oregon coast. If you're thinking you don't need to be in great shape if you're only doing a three-day stretch, you may be wrong. Again, day hiking is a great alternative, especially if you have two vehicles and can arrange long one-way hikes.
Three, there is no stretch that is not incredibly scenic--no part of the coast that is better than another! Seriously. I will say that the dunes, between Florence and Coos Bay, get a little monotonous with no dramatic headlands to break things up, but it's still sweet to be able to hike so far without encountering a road or town.
Four, how comfortable are you with attempting to hitch rides across river mouths? Alternately, are you willing to call up charter boat outfitters in advance and negotiate a fee to be carried across river mouths and stick to the schedule you arrange with them? If not, avoid the big bays or you'll be walking a long distance (unless you call a cab).
Here are some more specifics, north to south, that might help you choose where to undertake a backpack trip on just a portion of the Oregon Coast Trail:
NORTH COAST
Any part of the trail from the Columbia River to Garibaldi could make a fine short trek, but study my blog and plan where you are going to spend the night (camping options here are somewhat limited).
Between Pacific City and the north end of Lincoln City you can't avoid doing some (or a lot of) road shoulder walking. On the other hand, I would not recommend bypassing the hike over Cascade Head (regardless which route you choose).
Between the south end of Lincoln City and Devil's Punchbowl you will be walking on the road shoulder a fair amount. Much of that is a side road (at Otter Crest), however, and not busy (almost like walking on a paved bike trail), and you can eliminate some walking alongside US 101 if you can hitch a ride across the mouth of Siletz Bay with a recreational boater.
CENTRAL COAST
Between Gleneden Beach (south of Lincoln City) and the Siuslaw River at Florence there are no big bays/river mouths to go around; Yaquina Bay (at Newport) and Alsea Bay (at Waldport) are quickly crossed on scenic bridges, and ditto for the Yachats River at Yachats. This stretch is not very remote, however, and there is a fair amount of unavoidable road walking between Cape Perpetua (south of Yachats) and Heceta Head (north of Florence), although Cape Perpetua is stunning.
The Oregon Dunes are remote and lovely but, as I mentioned, a bit monotonous, and there's the Umpqua River to cross in the middle (and Coos Bay at the end); either prearrange a ride with a charter boat operator or plan to take your chances hitching a boat ride.
SOUTH COAST
Then we have the wild south coast! From Seven Devils State Recreation Site (or Whiskey Creek just to the south) to Humbug Mountain State Park, you can walk a long way with no road or town encounters or major river crossings but for a brief stretch at Bandon and Port Orford, although camping options are, as ever, somewhat limited, and the last several miles of beach between Bandon and Floras Lake are a tough slog.
The stretch from Humbug Mountain to Gold Beach is very scenic but includes a fair amount of road walking. I love the stretch from Gold Beach to Lone Ranch Beach north of Brookings: only one fairly brief stretch of walking on the highway shoulder (south of Crook Point) and an incredibly beautiful and varied coastline. From there to the end of the OCT at the California border you're mostly on road but for a short beach stretch just north of the border.
I hope that helps!
