Yesterday I upgraded from 5.7 to 6.4 and all seemed to go well. I had turned off the only extra module (ThemeSettingsAPI) and set theme to BlueMarine instead of Zen. I deleted everything from my public tree except for non-Drupal directories (I have several subdirs that contain content from a pre-Drupal site, not yet migrated into Drupal). I even deleted a directory 'drupal-5.7' which I was a little worried about, since it was empty and had no idea of its purpose.
I then copied the new 6.4 tree into place. The upgrade reported lots of info about the database, but nothing that looked like a warning. Afterwards there were 2 warnings in the status report -- needed to turn on update notifications (no surprise) and couldn't write to 'files' dir (no surprise, chmod 777, fixed).
One thing that worried me was that although it told me it had successfully detected my old version and would upgrade, it DIDN'T SAY WHAT THE OLD VERSION WAS. How do I know it really had successfully detected the old version? I feel an improvement is needed here -- I'm new to this site, so I hope someone can propose that.
The front page still has my previous recent articles, but the navigation menu has reverted. It now contains only the link to my contact page (unless I'm logged in as admin, in which case there's also all the standard admin stuff).