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SOFTWARE
software for home users.
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then:
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Try taking a look at Adobe's web site, and how they organize stuff. I've found them a very good jumping off point.
Personally, 40 links are overwhelming. But if you can do the above, and I think keep in one spot (like to the left) instead of seeding the links at the top AND the left (like microsoft.com), then you'll be better off. Multi-locational links are tough to figure out, unless there is a STRONG hierachy going on.
This doesn't answer your question about using sidebar navigation or not, but it could help your users identify where they are in this big pile of content. Good luck.
With 40 links to fit in, you might get away with 6 categories, but I'd definitely try for no more than 7. And then limit each category to 7 links.
I like the Adobe scheme. I'll bet they worked very hard to come up with those categories.
I also think Amazon has done an amazing job organizing their page - but they did resort to a "show more stores" tab, and I'll bet that which store get hidden in that link has a lot to do with their customer database, including your most recent purchases.
Sometimes in situations like you've described, there are one or two real oddball links that just won't fit naturally into any category you can copme up with. I once worked on a site where there were two oddballs like that. What I did there was to treat those links as something completely "other"... a totally different visual treatment. Since they were "other" any way, this makes complete visual sense in describing that site.
So the main categories looked like a set whose members were all one kind of thing (in your case, categories of links) - and the eye naturally sees them as a group. The two oddballs were then at the bottom, as a different kind of thing which you could either tune out or focus on.
Pulldowns may be another option, but I never cease to be amazed by the number of people who simply cannot find the item they want on a pulldown list. I guess some folks just don't realize there's a full list of options to be seen on a pulldown menu.