There's tons of crap that Maya doesn't manage that can seriously screw up file handling. One of the classics is imagePlanes, these just have a habit of hanging round, we've had some scenes in the past with 100,000+ just because of the amount of times artists use standard files and import, which gets imported and so on. Just take the 'Dag Objects Only' off in the outliner and look what you've got left in your scene (it can be frightening sometimes!)
We manage the hell out of scenes now, intercepting them on file load and opening up a scene Health report so people know when things are starting to get bad.
CEO & founder : Red9 Consultancy Limited
http://red9consultancy.com
Author: Red9 StudioPack / Autodesk Masterclass 2011 - Live Animation Binding
http://area.autodesk.com/siggraph2011/masterclasses/class2
http://red9-consultancy.blogspot.com