I haven't added any indexes for my main site (oxle.com), and to be honest I have no idea where to start. I'd like to increase performance of the search function though, as that function seems useless in the current form (for me at least). Instead of searching on the forum itself I use Google to search my own site (in the form of "site:oxle.com + keywords").
Even indexes will not fix the search as it is, the whole of the search code needs re-writing to be optimised for the database in use, and if possible freetext indexing should be used. There are mods around that do one or both of those things.
There is no tried and tested index additions, since they really depend on how the majority of users use the forum, the only way to find out is to run the sql profiling tools while your forum is being used and then sql will tell you if you need to create/change your indexes.