If you want to remove h2 from your tinymce dropdown, try to delete it from jsparty/tiny_mce2/tiny_mce.js and tiny_mce_src.js or jsparty/tiny_mce2/themes/advanced/editor_template.js and jsparty/tiny_mce2/themes/advanced/editor_template_src.js.
Of course is not good to change core files, but at the moment there is no another way to do it :(
You can always create your own settings module, where you can add your important core settings. It's takes time, but after you need only to compare some files in your settings module with update files - thats makes updating process more easy.
@web.take.away: "Of course valid elements depends what you need to add. In my example I added lightbox on the images links."
You mentioned adding lightbox to TinyMCE, I'm very interested in how you achieved that and can't see anything like that in the code you posted.
Putting LightBox or FancyBox etc. in the template is quite straightforward and I would love to give editors the possibility to insert a "zoomable" pic within TinyMCE.
You add "TB_iframe" to the insert-image-dialog but you surely have done some more? Fields in the DB-structure, selection of the "big" picture etc.?
Can you give some more information on specifically that?