I've not found a good way to do annotations or any sort of free-form drawing on Gimp, but I do tend to grab the image and toss it into Visio for annotations there. There I can use the drawing tools, and stencils like Callout boxes then to highlight and annotate visually.
There are the web-based visio-ish clones like LucidCharts you could use in place of visio too. Sadly visio is still a quite useful tool even though it is on windoze only.
I use Master PDF Editor as well for manipulating PDF's, it's pretty awesome for that. Under linux it's free for non-commercial use, but windoze they restrict your saving ability for pay unlock.
-mb