Yes, there are many ways.

The easiest for what you are doing would be to use the open-source program DoubleCommand.

Here is a view of the interface:

As you can see it is extremely customizable. If that doens't fulfill your needs, there is also Karabiner (formerly known as KeyRemap4MacBook).

There is also a shareware program called LiteSwitchX that completely replaces the switcher with an even cooler and more customizable one that I will eventually get around to installing.

I hope this helps.

You can also use a combination of two programs: Application Enhancer (by Unsanity, free) and PullTab (open source and free). PullTab ONLY removes the shortcut from use so it depends on exactly what you're looking for. Application Enhancer (APE as it's commonly called) also has WindowShadeX and MenuMaster, which I recommend at least checking out.

I'm going to continue looking for a non-third party way to disable this, I may edit it again.

BONUS

Also, press cmd+` (command + backtick: backtick is directly under Escape, with the tilde) to cycle through the current application's windows rather than cycling through each application.

One more thing:

When you are in the application switcher, you can also press Q and/or H and the currently selected application will be quitted or hidden.

There's no way to do this. Besides, Ctrl-Tab is already used in some applications, like Safari, to e.g. switch between tabs.

You can use Witch for a custom application switcher and use Ctrl-Tab for that.

In System Preferences » Keyboard » Keyboard » Modifier Keys, you can switch positions of the keys. This will however change all keyboard shortcuts (e.g. Cmd-C for copy effectively becomes Ctrl-C).

You could use a private.xml like this with KeyRemap4MacBook:

<?xml version="1.0"?>
<root>
  <item>
    <name>test</name>
    <identifier>test</identifier>
    <autogen>__KeyToKey__ KeyCode::TAB, VK_CONTROL | ModifierFlag::NONE, KeyCode::TAB, ModifierFlag::COMMAND_L</autogen>
    <autogen>__KeyToKey__ KeyCode::TAB, VK_CONTROL | VK_SHIFT | ModifierFlag::NONE, , KeyCode::TAB, ModifierFlag::COMMAND_L | ModifierFlag::SHIFT_L</autogen>
  </item>
</root>

http://www.hcs.harvard.edu/~jrus/Site/Cocoa%20Text%20System.html has some great info about changing the default key bindings for Cocoa applications. Unfortunately I could not figure out if there is an action method for the switcher.