MediaMonkey uses Album and Album Artist to define what is an Album. When syncing to iDevices it will set compilation flag in the iDevice database.

What I've done for compilation albums is set the Album Artist to "Various Artists" for the entire album while leaving the "Artist" as the specific artist for that song. I've found that this works very well, and provides me with more flexibility that iTunes "Compilation" checkbox.

It would be nice to have an attribute per album that indicates whether it is a compilation or not. Further, the attribute would then be inherited by the songs in that album. The attribute would be visible and changeable in the 'properties' window in the same way as things like 'genre' or 'year'. Search and other organizational mechanisms should be able to make use of this attribute.