Harris and Lewis. Just gorgeous - some of the best beaches in the world. Would be my number one recommend. (Not as touristy as Skye.)
Iona is peaceful, reverent and spiritual.
Glencoe/Rannoch Moor, bleakly stunning and very powerful especially if you research the massacre. Most of the Highlands is gorgeous to be honest, especially if you get a clear day for views. The Road to the Isles is rightly famous. As is the Glenfinnan Viaduct if you are or have Harry Potter fans but you do need to book the train trip well in advance. If you have active kids there's lots of activities round Aviemore to wear them out for a while.
Mull is lovely - Tobermory was Balamory and is cute but also go across to the west side where it's less popular. Islay had a great whisky tour done on bicycles, we were a bit wobbly by the end 
Perthshire is "tamer" beauty, think rolling green hills and pine forests. Tumnel Valley, Queens View, Pitlochry area very popular esp with the beige slacks and afternoon tea brigade but there's lots to see and do.
Loch Lomond is lovely on a warm sunny day but half of Glasgow will decamp there if the weather is good so you may need to travel round to find a quieter spot.
Edinburgh is such a beautiful city. The architecture and history are top notch. I'll never forget coming out of Waverley station for the first time and seeing the castle on the rock all lit up at dusk for the first time. Magical. Lots of cultural stuff all year round (it gets incredibly busy during the festival in August of course).