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With the 5.1 tree on my laptop sql/mysqld.cc takes 41s, and I have a patch which drops it down to 20s (which should end up in 1.3). There is also a small patch for gannotate which should be in the next release as well.
As a point of curiosity, are you using these over a remote X connection? I've heard statements that GTK over remote X is rather slow, even on the local network.