Like a lot of people, I'm finding Logos's indexing takes over my comparatively old Mac, even since I've upgraded to 2GB of memory. The problem seems to be more memory than processor-bound - it does seem that the indexing process grabs all the memory it can, then starts thrashing, particularly if you then load something else.
The following changes would make the situation vastly better (in decreasing order of importance):
1. If you pause indexing then it needs to free up most of the memory used: if it's sitting there hogging 400M of RAM, then the computer is still unusable.
2. An option to the indexer to use at most a given amount of memory and no more. It seems to be capable of doing this anyway (it never used more than about 200M before my memory update).
3. An option that indexing should be manual: if the system wants to reindex, then it should ask you first, as is the case with reinstall for new versions.