There's a well-known and very annoying bug in Safari 1.0 (I don't know if it's been fixed in the 10.2.8 update) that results in new windows being opened offset slightly down and to the right. The only fix I've seen advertised so far involves installing the Application Enhancer panel, something I'm not overly keen to do.
On further investigation, it appears that windows are correctly positioned if they are smaller than the screen width (i.e. don't have a width greater than 1024 on a 1024x768 monitor like mine) but get confused if they are set to be any larger, or are positioned outside the screen boundaries (if they are dragged to the right, for example - something I often do by accident.)
My solution is to set Safari's prefs to always start more or less fullscreen (leaving room for the dock) by issuing the following command:
defaults write com.apple.safari "NSWindow Frame BrowserWindowFrame" \ '0 0 1024 685 0 0 1024 746'
The first two zeroes tell Safari to open the window at zero pixels from the top and right (so no offset, as it should be) and the next two values tell it that windows should be 1024 pixels wide and 685 pixels long. Your usage will vary here depending on your display - the important point to note is that the Safari window size should not be greater than your screen resolution.
You can fiddle around with this command until you find a setting that you like, and then save it as an executable .command file to make a quick shortcut, as a command line alias in your .tcshrc or (as I do), include it in your .login script.[robg adds: I don't think the window offset is a bug, I believe it's a feature -- when you open a new window, you can see both the old and new windows at the same time. However, if it annoys you and you don't mind using full-screen windows, this should fix the problem (though I didn't experiment with it extensively).]