Bubbling I prefer pencil so when a mistake is made I can correct it. If its a multi page bubble and I know the pencil lines are all set I will then go over it with a hilighter.
For Highlighting, I use Bic Brite liner. The tip is small enough to make it easier to highlight one line at a time . It doesn't seem to bleed either
For notes and underlining, I like Pilot G-2 0.38mm ultra fine point pens. I like them since they are very fine point for when you have to squeeze a lot of text in a small place . Plus I have bad handwriting so anything wider ends up looking smudged or I run out of room. Although it doesn't have as many color options as .50 or wider.
Thanks for any suggestions!