The questions which are in different color are those ones, which have one of your favorite tags.
From What do “favorite tags” and “ignored tags” do?:
- Questions with these tags become highlighted on the front page.
- Questions with new activity are shown on stackexchange.com/filters.
- In the review queues, questions from these tags are shown to you before other questions.
The actual color is different for various sites - it depends on the design and color scheme of the actual site. (For example, they are highlighted with different color on Mathematics than on MathOverflow.