The Great Glen Way is a good one, I worked along the route for the last 3 years before moving on to a more exotic location (Shetland), having said that tho, its not really challenging with a lot of the route being along forestry roads. An excellent walk is the ridge above Loch Lochy, which takes in some staggering views (when you get the weather) up and down the Great Glen, there are some narrow sections but on the whole its a pretty easy ridge (when compared to the likes of the Aonach Eagach and the Cuillin Ridge) and good if you have never done one before.
Not knowing your hiking/walking experience level makes it hard to reccommend a set of walks that you would find challenging, sorry its the Mountain Leader in me. The Pap of Glencoe is a grand walk, The Two Gullies takes you around the base of Buchaille Etive Beag are good walks in Glencoe, on Skye there is Bla Bhen a knee crunching descent to say the least, 7 Sisters in Glenshiel, there's also a mammoth amount of walks at the head of Glen Garry, around Inverness there's Slioch, the area is full of walks large and small but each as rewarding as the other for lots of different reasons.
If you can I would suggest getting hold of the Ciccerone Guides 'Walking the Munros' volume 1 and 2 as these will cover the areas that you mentioned above. Then get hold of the OS or Harvey Maps you need and the ever important compass (although remember that this isn't going to work as well if you head into the Gabbro (Black Cuillin) on Skye as the rock is magnetic and monkeys about with the compass) and make sure you know how to use it (again its the ML/Ranger in me that makes me say such things not a reflection on your ability in the hills). As the others have said watch the weather, but there are a good few places in Ft William that display the Mountain Forecast so keeping tabs on that should be easy enough.
Hope all thats of use