Thanks everyone. Based on your comments, I now see "rabbit-trails" the having two very different flavors:
1) Those that come up while I am doing focused tasks:
The rabbit-trails that come up when I am doing focused stuff interrupts my flow. However, they may still be taken care of based on a predefined set of four questions:
a) How much focus do I need?
b) Anticipated length of time? (<2 minutes)
c) Maximum # of steps? (3 steps)
d) worthwhile to go further? (yes or no)
Of course, emergency tasks that can't wait take #1 precedence no matter what.
2) Those that come up while I am doing general tasks:
The rabbit-trails that come up while doing tasks are actually quite normal, and the way things actually get done. As long as I keep the entire set of next actions and all my contexts in mind while I am pursuing my rabbit trails, and ensuring that the rabbit-trail activities are the best/most natural activities at any given moment, then all is good.
Thanks again for your ideas everyone. They are very helpful. If you have more, please post.