Exhibit #2: Why doesn't Apple use cmd+D for Downloads? Because they used cmd+D for "Add Bookmark..." Oh, of course. Wait, what?! What sense does that make? The answer is none. It would make sense to use "cmd+A" for "Add" except that cmd+A is a system wide shortcut for "select all." The next logical thing is to use "B" for "Bookmark," not "D" just because it was the next available letter after "A" was taken.
Exhibit #3: I have a theory that no one at Apple uses bookmarks, considering what lousy support Safari has for them. Have you ever tried to manage your bookmarks in Safari? You can't even click to sort them. In addition, there is no keyboard shortcut for "Show All Bookmarks." However, once we've changed "Add Bookmark..." to cmd+B, it seems to make sense to make "Show All Bookmarks" equal to cmd+Shift+B.
If you hold down the Alt/option key while in the "Bookmarks" menu, "Add Bookmark..." changes to "Add Bookmark to Menu." So, once we've made the rest of the changes, it makes sense to set that to cmd+Alt+B.
Note: when referring to keyboard shortcuts, the standard practice is to use uppercase letters even if the keyboard shortcut does not include Shift. There is a difference between "cmd+B" and "cmd+Shift+B," but the proper way to refer to it is "cmd+B" not "cmd+b," according to the way Apple does it.
The next several have to do with making Safari features more easily accessible.
I remapped Quit Safari because I was constantly hitting cmd+Q when I meant to hit cmd+1 or cmd+W. Truthfully, I hardly ever quit Safari, so I wanted to make sure I remapped it to something I was very unlikely to press by accident, and cmd+Alt+Q fit the bill perfectly.
One of my favorite Safari features is "Merge All Windows," which will take all of the tabs from separate windows and turn them into tabs of one window instead. There is no keyboard shortcut for this by default, but cmd+Shift+M seemed a logical, and available, choice.
The "Activity" window can be helpful (although the window is weirdly non-resizable and has a column that usually isn't visible unless you horizontally scroll), but for some reason, I never remember cmd+Alt+A and always use cmd+Shift+A, so I changed the shortcut so that it will actually work the way I think it should.
"View Source" is cmd+Alt+U? Why? Because Apple wanted to make sure that I never ever remembered it. That's really the only explanation that I can come up with. Obviously, cmd+V wouldn't work because that is used for "paste," but cmd+Shift+V is a perfectly good alternative. It also has the advantage of being a mnemonic that a normal person might remember and not just someone who has been trained to think the way Apple thinks.
To change the Keyboard Shortcuts for Safari (or any other app) in Snow Leopard, go to System Preferences » Keyboard and click the "Keyboard Shortcuts" tab. Then click "Application Shortcuts" on the left column and then the "+" to bring up the shortcut editor. One very important note: you have to enter the "Menu Title" exactly the way that it appears in the menu. "Add Bookmark" is not the same as "Add Bookmark..." or "Add bookmark." Usually (but not always), each word is capitalized, and any menu item that brings up another window ends with "..." (That's three periods, not an ellipsis.) Be sure to check the menu item that you want to replace, though. You should not even need to restart the app to have the new menu item appear.