We are considering using Business Objects tools such as Web Intelligence Reporter as a report writer, query, BI tool for use with Baan. How easy is it to do cross company reports for the
end user or for the developer? One client reference apparently
is doing multiple query/reports for each company and then combining them, which appears to be somewhat clumsy to me.

Business objects is certainly not the right tool for queries over different companies etc. You should consider Croko Reporter for 3 reasons:

1) It is using Crystal designer for designing the report
2) Croko retrieves faster data out of the database then any other report writing tools
3) Croko can read in the datadictionary, something which BO is not capable of doing
4) Croko Reporter is at least 5 times cheaper then BO.
Check out : http://www.croko-reporter.nl

I'd agree that BO is not the way to go. Crystal has changed licensing over the years so I'd be concerned about potential licensing issues going down the Croko route...

Why not go with Crystal? It's also a solution that Baan endoreses. From what I've seen customers are pretty happy with it...