I've been using HTTrack for several years now. It handles all of the inter-page linking, etc. just fine. My only complaint is that I haven't found a good way to keep it limited to a sub-site very well. For instance, if there is a site www.foo.com/steve that I want to archive, it will likely follow links to www.foo.com/rowe and archive that too. Otherwise it's great. Highly configurable and reliable.
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