Here is a run-down of how I made good use of my points and awards over the holidays.

Hamamatsu Comfort 12,000 points for a room. Free breakfast. Points cost me about ¥6,500 through Daily Getaways.
Higashi Kanda Comfort 12,000/room. Free breakfast.
The Strings ANA Intercontinental. Two free welcome drinks at bar (we had champagne). Free night cert from Chase card (fee is $49/year).
Hyatt Regency Nishi-Shinjuku (2 rooms). One with a free Chase night ($75/yr), the other 12,000 points.
New Year's day, Marriott Fuji Yamanakako. Triple room. Free booze and snacks in room since lounge was closed. Free breakfast for two as a Titanium, paid ¥4,400 for the third person.
Chubu Airport Comfort 8,000 for a room. Free breakfast. Cost ¥4,400.
Four Points Chubu Airport. Paid cash, ¥14,000 and used a Bonvoy suite upgrade for a nice junior suite. Free breakfast for two as a Titanium.

Comfort hotels using the points I bought are the best deal, especially when there are 4 of us and breakfast often fills us up until mid-afternoon. Award pricing is the same for one or two guests. Parking ranges from free to ¥2,000 a night, with the average around ¥800. Rooms vary in size a lot. Some hotels have queens and twins, others only a single bed or a double bed. Some have library lounges which are nice places to hang out.

Marriott, Courtyard, Westin and Four Points have all impressed me with their breakfast offerings (Sheraton Osaka not so much). Adding in a third person though is pricey, usually ¥3,000-¥4,000, which could buy a decent dinner outside the hotel.

Booking Hyatt is usually pretty easy, but most of the ANA Intercontinentals in Japan are over the 40,000 limit much of the time (variable pricing), which makes using an award night a challenge.