Alexander,
I think you may have answered your own question. If Matt Cutts says they are fine but don't use them to increase your potential keyword percentage, I wouldn't do it. If you utilize a tag cloud to help navigate your site/posts/pages then go for it.
As always, it always comes down to quality, unique content. There is no way of getting around it, so just build excellent site navigation, and proper linkage in your homepage content and you're set.
Best of luck.