Annotating is by far my favorite intensive reading choice. I like to demonstrate this beforehand on the document camera for all to see, as well as after the activity to review.
Locating main ideas
Underline sentence in each paragraph that summarizes the main idea. Show students various locations for main idea sentences: first sentence, second sentence, last sentence, or just repeated ideas throughout the paragraph.
Marking supporting details
Underline or circle key words/phrases in each paragraph; note the key transitions like "however", "but", "yet", "despite" if present; write the main idea in the margin. This works well for passages that give contrasting ideas (supporters vs. opponents).
Mapping/Outlining
Help students identify the main idea and supporting ideas by analyzing the structure. Create an outline of the entire article. Create a map of the article (main ideas, support, cause-effect, etc) on a poster. Using the map/outline/annotation to write a summary or paraphrase of the whole article. Or using the map/outline/annotation to answer the comprehension questions.