Large MU site architecture questions

We are going to use WPMU as the CMS for a good size website. (200-300 pages) We want to leverage the BuddyPress stuff as we move forward – but am wondering how others have handled the architecture.

One thought is to have the different “sections” of the site be a separate “blog” in MU and then each section could have it’s own theme and feel…but then another part of me says to stick in one big install.

If anyone has thoughts – I’d really appreciate them. WordPress is faily new – I’m moving over from a history with .NET.

Again thanks,
tom