One way to do this is to add "markers" in the scene geometry file itself. You would use a specific naming convention on these markers (which are just pieces of geometry) to represent various things.
Add a sphere and give it the name "player_spawn_0" to represent the starting location of the player. Perhaps more helpful would be to add the player's model itself to mark the player spawn. What you use doesn't matter, as we'll see shortly.
When you load in your game, you would then check for these markers in the model file itself, note their locations, name, properties, etc then.
Once loaded, delete them from the model so they don't draw.
Most modeling packages allow you to add data to objects (color, texture, etc) so you can use these properties to your own properties. All of the major modeling packages also support you adding arbitrary data to objects so you wouldn't have to stretch yourself trying to finding ways to encode data on your objects. You also get the benefit of editing right on top of your level instead of making little adjustments to marker positions until they are in the right spot.
Other than that, there are a number of free or cheap level editors that output to a neutral scene file, like http://www.getic.net/
Exploiting your modeling software is probably the easiest way other than building your own editor however as you don't have to add another set of tools and file formats to your pipeline.