Hi sneather, there's a script here which will separate a bunch of objects with the same name into different names with _1 and _2 appended on to them:
http://moi3d.com/forum/index.php?webtag=MOI&msg=3114.5

I'm not sure if that helps but if you select all your objects and then give them all a name, then run that script it should give you separate slots in the "Objects" section of the scene browser for each individual object.

But you may not want to do that if it's a complex project like you mention since you will then end up with a tremendously long list of names...

- Michael