Try using the Note Flags. This of course can be sized according to the text
size of your note. 10pt will have a small noteflag, and 32 will be large. You
can even customize the note flags to create Arrows by going to
Format > Note Flags > Customize My Note flags...
select an undefined, or defined (if you like) and change it by double
clicking on it, then choose the symbol, the default font and color you wish
from the popup!
Then when you want to make a flag ctrl+1 (or whatever number you set up) is
the keyboard shortcut to add it!
And if you're using a tablet pc (which is what one note was designed for,
but is also good on normal computers) you can just draw a circle around your
note. Highlighting can also be a good way to make your notes stand out. (agh
can't find keyboard shortcut for this. CHRIS!! We need this!!!)
-James