IMHO WPMU, BuddyPress and bbPress works well if:
– You set a wildcard domain (in my test site subdirectory based instalation doesn’t work)
– BbPress table is in the same database as BuddyPress, WPMU and i. ..
– BbPress has the same prefix as WPMU. For example, if you use a standard prefix to the WordPress table (for example wp_) then for bbPress give wp_bb_