That is the question...
The game has a great tool called 'Ask your stock broker', which will let you see at a glance what blogs you hold shares in will benefit from reindexing. Unfortunately, if you're looking to reindex, say, a blog that links to you, there is no easy way to tell if it will go up or down in value. Do not assume that if your blog is on the rise, that reindexing anything coming in or going out is a good idea.
I've found it handy to whip out the old calculator and punch in the numbers manually to see if it's worth it. I usually just enter up to the hundred thousand place (B$25,485,434.10 becomes 254, etc, no rounding), and total up everything over 100k in value. If this is greater than the blog's current value, reindex. If it's very close, then I'll redo the numbers going down to the thousands place (B$25,485,434.10 becomes 25485), and see what happens there.
If you're reindexing something that links to you, never reindex if the value is going to drop.