Since reading Buffy and SGA, I have been trying to leave positive feedback when I really like a story or an author. The ones I dislike or find boring, I just don't leave a comment. Just appreciate that there are people out in the 'aether', who are creative in their fan fiction. However, I too have been reading it forever and it seems as if most stories tend to repeat plots with which I am already familar. Think many of us have certain genre's that are preferred, and ones that are not to our taste. Now that I am on lj it is much easier for me to give feedback, except on fanfiction.net. For some reason it won't except me when I hit the feedback prompt.
And as you say, some writers have a lot of feedback, but usually if you respond to them with positive comments, they almost always reply with a thank you or more. So feel free to comment.