The threads get two colours. Depending on the theme you're using.
For threads which have not been checked by you since they had 'activity' (e.g., thread post and/or comments), the thread title will be a more 'attention grabbing' colour, to indicate un-read content within it.
For threads which have been checked by you since they had 'activity' (e.g., thread post and/or comments), the thread title will be a more 'neutral' colour, to indicate that you have opened the thread since its latest activity.
Ohhh, in that case, you're talking about the numbering?
Arctic has the two colours, previously described, as a pale blue and black.
What you might be seeing is thread voting. On Arctic, threads which you have upvoted are gold/yellow, whereas threads which you have not upvoted are grey. To the left of each thread, that is.
@The Conservationist Yes, the gold/orange colour is on the numbers with the up arrow at extreme left of a thread, so I guess it just indicates threads I've upvoted.