So I looked around a bit and what I can already say is that it improved. Now it's more natural and comparable to other emulators.
Though there are a few things I'd like to say.
In my opinion the positioning of "Debug" should be between "Movie" and "Help" so that it goes: File, Options, Tools, Movie, Debug, Help.
I would also switch the "Sound" and "Input" inside "Options" as it is important to configure the Hotkeys as you first use the emulator.
I don't know how often it's used, but Debug > Logging > Print/Trace > (
a lot of things)... looks like a lot of work to activate specific options and deactivate ones you don't want. Maybe another window with some checkboxes would be easier to use.
But other than that, I really like the new grouping of stuff and the more familiar look of the menu.
edit: I forgot one thing, I don't like the fact that hourglass has a "Stop Capture" option. I think it should only be there if you are actually recording or maybe it should replace the "Record Video" option. I'm used to stop the recording by going exactly where I started the recording in the menu (which didn't work in hourglass r81, making my encodes too long).