Did you know that you can manipulate a game objects collider in the scene view by holding down the 'Shift' key. Holding shift will display the colliders control dots. Just drag the dots to adjust the collider!

Hold the 'V' key while the translate tool is active and you can drag an object by it's vertices and snap that vertex to another objects vertex!

The inspector window contains a small lock icon in the top right of the window. If you select a game object and click the lock the inspector will be locked to that object and will not change when you select other objects. Click again to disable the lock. This allows you to have multiple instector windows open with locks to different objects.

To allow the user to undo actions that are performed by a custom editor script you can use Undo.RegisterUndo. 

foreach (var item in Selection.transforms)
{
    Undo.RegisterUndo(item, "Move " + item.name);
    var pos = item.position;
    pos = new Vector3(activeObject.transform.position.x, pos.y, pos.z);
    item.transform.position = pos;
}

If you want to take advantage of functionality that is provided my menu commands you can use EditorApplication.ExecuteMenuItem in your editor scripts to execute them.

Are you working on a large project but dislike how many objects you have to weed through in the hierarchy window? You can create editor scripts that change the objects Object.hideFlags property to hide or show the object in the hierarchy window.

var item = Selection.activeGameObject;
if ((item.hideFlags & HideFlags.HideInHierarchy) == HideFlags.HideInHierarchy)
{
                item.hideFlags = item.hideFlags ^ HideFlags.HideInHierarchy;
                item.active = !item.active;
                item.active = !item.active;
}

Notice that item.active = !item.active is specified twice. Currently in unity 3.5 you need those 2 lines of code for the game object to hide and show properly in the hierarchy window.

Wondering how to save player preferences across sessions or save settings for an editor script to use? Check out EditorPrefs & PlayerPrefs.

If you are writing custom editors for unity and you need to have a way of editing the tools settings you can have those settings show up in the Unity Preferences Window "Edit -> Preferences...".

Just create a new editor script that has a public class and add the fallowing lines of code ...

// Add preferences section named "cbxTools" to the Preferences Window
    [PreferenceItem("cbxTools")]
    public static void PreferencesGUI()
    {
        // Preferences GUI
        cbxToolPreferencesConfig.Instance.DrawGUI();
    }

If you are creating custom editors for unity but only want the gui for that editor to be drawn in the currently active scene view try this ...    

if (SceneView.mouseOverWindow.GetInstanceID() == SceneView.currentDrawingSceneView.GetInstanceID())
        {
            this.DrawGUI(SceneView.currentDrawingSceneView);
        }

If your suddenly finding that Unity will instanty terminate while running your code, check if you are invoking any infinite recusion loops. This has recently happened to me and it was a bit of a pain to track down with Unity 3.5 instantly terminating. Hopfully the Unity team will handle the infinite recustion issue in a future version.