I will build several community sites that somehow similar structure. I will use buddypress. I am new to Wordpress I have used Drupal before. Currently buddypress 1.6.1 version states that it works with multisite configuration. What about other popular plugins do they also work with multisite? In Drupal multisite is straightforward, but I have read some problems with Wordpress multisite plugin support. Which one is less trouble multiple distinct setups for each domain or using one instalation with multisite configuration.
All properly written plugins work on multisite too. You should still test each plugin separately and in combination with others on a development installation.
Keep in mind, the wordpress.org plugin repository is just hosting many plugins; there is no quality control – read the code before you install anything. Use the plugin Log Deprecated Notices and check each plugin for these notices. They are usually (but not necessary) a indicator for wrong code.