suicidal multisite database queries

It has come to my attention that querying the multisite database to get information from all its sites is not a good thing if you have a lot of sites.

Plugins that do things such as list all the sites in a multisite, or publish all recent comments, rely on the db-querying function get_blog_list, which has been deprecated for its “suicidal” tendencies.

I have read about the transients api, but don’t understand how to use it, and apparently there is some question as to whether that even would work in this case.

I need more information about the advisability of and alternatives to querying the database if you have a large number of sites. Please kick this over to the WP-Advanced forum if necessary.