Check out http://www.calmac.co.uk/ for your tickets to get you round the islands - they have a specific island hopping ticket which may be what you are looking for.
Depends on how long you have and what you want to see but I would recommend Skye, and Islay for the Laphroig distillery. I like Mull and definitely a trip to Iona is wonderful.
Also the roads to the Islands can be beautiful, such as travelling round the Ardnamurchan to get to Mallaig to catch the ferry to Skye. A really nice journey (excluding Fort William !!).
The roads in the Highlands are not the easiest, and many of them are single track, so this will affect how far you can travel. Also, in peak times, accommodation can be a little difficult, especially in rural areas.
If you go in summer, watch out for the clegs! They are vicious biting winged things and they can hurt! about 5 years ago