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I think that depends on what is important to you. If for example think that the "relation" with another blog/webmaster is more important then the amount of traffic that a blog send then you should place the links that point to your friends blog at the top. If you are trading traffic then you should put the blog that brings in the most traffic at the top.
You can indeed also split it, your friends blogs under "my friends header" and your traffic link partners under "link partners".
The same applies to blog directories, if the blog directory sorts blogs on incoming hits, then you should put these blog directories somewhere at the top of the blog directories, cause when surfers click on these links your blog is moved up at the blog directory causing your blog to get more surfers.
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