Install Filebox from extras-devel (it's a safe app don't worry). Connect your N900 to your computer in mass storage mode and open the N900 (not the memory card) then create a new folder, call it Custom or something. Then unplug it, open filebox, tick the 'up' arrow to go two pages back, then it's opt/usr/share/icons/hicolor/64x64, in there you'll see what you want to change, like the phone icon is general_call and conversations is general_SMS. Whatever you want to change, hold the icon until a box pops up, tap 'copy', then hit the 'home' icon to go back to MyDocs, open the custom folder and the second icon on the right is clipboard, hit that, tick the icon you copied and then the top icon (paste).

Reconnect to the computer, open Custom, drag the icon(s) to the computer - that's your backup in case it goes wrong. Delete the icon from Custom, drag the custom icon to it and rename to be exactly what the original was, copy then go back to usr/share/icons/hicolor/64x64 and hit clipbaord and paste. It will say 'do you want to overwrite', say yes. Reboot and you'll notice a new icon.

The desktop switcher icon is different, they're in /usr/share/pixmaps/desktop-switcher/switch_left.png
/usr/share/pixmaps/desktop-switcher/switch_right.png
they go left and right, for '1' '2' '3' just change to that. 'Home' will be switch_1 I think, you can easily see what to make it by opening the folder in filebox and seeing what it's called.

Once you do it once it's easy. To break it down:
Copy the original icon and paste it in Custom (the 'home' icon in filebox takes you to your MyDocs, where Custom will be when you make it.)
Rename the new one to match the original, put in Custom, then copy it.
Go to the respective folder, for email, sms, phone, contacts etc that's opt/usr/share/icons/hicolor/64x64 and clipboard>paste, 'yes' to overwrite. Reboot.