Lots to do. Some items, icons can only be changed by editing IE related files, listed here. But even with just tweaking there's a some nice things to change. Plus, some tools are available to help with some of these:

With IE4+ installed you can define a bitmap to be displayed behind your toolbars, in explorer and internet explorer:

• Open regedit and find the key
  HKEY_CURRENT_USER\Software\Microsoft\Internet Explorer\Toolbar;
• Select, and on the right, rightclick and add a new string value, name it "BackBitmap";
• Rightclick on it, choose modify;
• Specify the path to your bitmap (.bmp !) and close.
  
  If you've got IE5 installed, the BackBitmap still works then. But you may insert another string value called "BackBitmapIE5". The normal one will work for your general explorer windows; the new bitmap is specific for IE5 and Outlook!
  
  Running IE6, or using Windows XP, though it comes with IE6, the BackBitmapIE5 value is still the same, but the string value for the explorer toolbar is now called "BackBitmapShell" (same key). Still, BackBitmap works too.

The animated throbber in the upperright corner can be fully customized by creating a filmstrip bitmap with frames and creating some registry keys (for the logo in your explorer windows, check here). Main image has to have a width of 26 pixels (the small logo as shown on the right) or 38 (the big version). The height must be an even number of times the width. Read somewhere it has to be at least 12 times the width (not sure), so let's say it has to be something like 26x312 or 38x456. Now you have 12 squares which are the different frames of your animation. For a smooth animation, repeat every frame once. The first and upper frame is shown when IE isn't busy or you're not connected. (If you need an example (as shown above), it's here (5 Kb).) Open RegEdit and go to: Click on it once, and on the right, add a new string value (click right there). Name it 'BrandBitmap' (without the quotes), or 'SmBrandBitmap' if you made the small one. Then, rightclick on it, choose modify and enter the path to your bitmap. Close and restart.

If you've got IE5+ installed , you're able to use a seperate bitmap for the non-animated logo. You may even need to do so, if you experience borders along the (brand)bitmap. It's got to be 26x26 or 38x38 and is displayed when the browser isn't busy. Insert a string value called "SmallBitmap" or "BigBitmap" at The animation is displayed a little different too. The first 4 frames are played when browsing starts. Frame 5 and more are played until browsing stops.
A little tool to convert animated .gif to a vertical (or horizontal) frame sequence is bitstrip.

Change titlebar text in IE and Outlook. There's some simple registry settings for this, but different versions of IE and OE use slightly different names and/or different places to store these settings: While you're there, you might create another DWORD value called 'NoSplash', to get rid of the Outlook Express splash screen. Modify and set to 1. For OE4, you might just import this regfile.

Byblostas pointed out this registry key, that handles icon and text display concerning zones (in explorer and IE, lowerright side): There's some keys underneath numbered 0 - 5, representing the different zones IE uses for security settings. Byblostas found settings for the icons and displayed text are inside. The text settings are simple string values, easily changed. So are the strings for the icons, but notation differes with other icon settings in the registry. Normally that's something like "c:\windows\shell32.dll,14", meaning the 14th icon in shell32.dll. Replacing with the path to an icon (no comma) or .icl (comma) does the trick. But here notation is something like "...shell32.dll#0014", so the rules are different.

To link normal icons you should use the icons path then add #0002, for example: "...mydocs.ico#0002". Linking to a .icl is about the same, icon no. 0 is defined as #0000, then icon no. 1 is #0002 and after that it keeps on logically with a one icon shift. So for example "...basic.icl,15" should be "...basic.icl#0016". Icon no. 100 should be #0101.

Notes:

• This tweak applies to your normal explorer windows too. Any changes reflect in IE immediately, for explorer a restart is required.
• Conveniënt - Toolbar Control by beaker will change the settings for you (for now, only in 9x).
• Related: to make the "My computer" zone appear in the zone security page (double-click zone icon) change its dword "Flags" value from 21 (33) to: 1 (1) in the related registry key (..\Zones\0), but be carefull to not lower your level too much though.

If you're running IE5+ on Windows 98/Me/2k or XP, it is possible to add items to the IE toolbar (2k/XP users, read below):

• Open regedit and check if the key
  HKEY_CLASSES_ROOT\CLSID\{1FBA04EE-3024-11d2-8F1F-0000F87ABD16}
  exists; if it doesn't (it should in IE5+), this tweak will not work!;
• Then, find the key
  HKEY_CURRENT_USER\Software\Microsoft\Internet Explorer\Extensions\CmdMapping;
• Note the "NextId" key, for the case of this example let's say it's "NextId"=dword:00002001;
• Rightclick it, choose modify and add 1 to the current value, for our example, change it to 2002;
• On the right, rightclick and add a new DWORD value, name it
  "{3037FC09-62A6-4446-AA30-BB9DB0CD9B65}";
• Rightclick on it, choose modify, and type 2001;
• Now create a reg file similar to the following:

REGEDIT4

[HKEY_LOCAL_MACHINE\Software\Microsoft\Internet Explorer\Extensions\{3037FC09-62A6-4446-AA30-BB9DB0CD9B65}]
"Clsid"="{1FBA04EE-3024-11d2-8F1F-0000F87ABD16}"
"ButtonText"="GetRight"
"Exec"="C:\\Communications\\GetRight\\getright.exe"
"Icon"="C:\\WIN98\\Application Data\\Microsoft\\Internet Explorer\\GetRight.ico"
"HotIcon"="C:\\WIN98\\Application Data\\Microsoft\\Internet Explorer\\GetRight.ico"
"MenuText"="Open &GetRight"
"MenuStatusBar"="Open GetRight"

• Import the newly edited reg file into your registry;
• To add multiple items add a 1 to the NextId key and re-edit the reg file above by adding a 1 to the the top line only. For the example, clsid would be {3037FC09-62A6-4446-AA30-BB9DB0CD9B66};
• Shampoo, rinse and repeat.

Notes:

1. Running XP Home edition, first line of the registry file should be "Windows Registry Editor Version 5.00" (not something you will break your registry with, though).
2. Running 2k or XP Professional, take the easy road. Open a run box, type "gpedit.msc". Browse your way down to User Configuration, Windows Settings, Internet Explorer Maintenance, Browser User Interface, and in the right pane doubleclick "Browser Toolbar Customizations". Appearing dialog will let your add any number of items you want.
3. !! Or, easy for all platforms, CustomizeIE takes care of all too. Great tool, add your custom buttons and/or menu items from a clean, simple interface.
4. This is particular useful if you don't want the extra "Links" toolbar added, to have links to sites you visit often there. At the Exec value, type an url, like "http://www.virtualplastic.net/".

It is possible to replace the IE "Search" left panel, showed when clicking on the related toolbar button. The replacement can be any html page, including search boxes for any search engine you'ld like. Links could also be used, to the web, but also to launch apps (check this). To change the url of the search panel you should use the regedit file provided in here, also including a readme and a basic example of search page.

Byblos created for us a VPToolBar for IE5+ you might find useful. It's got a button to go here directly (with some options), a search box that runs our search engine, and a couple of dropdown lists with links to forums, maillinks, hosted sites and some more. Get it here (57 kB), and give byblos/us your ideas.

Also worth mentioning is the google toolbar, that lets you quickly search in google from IE.