One thing I came across the other day was this:
code.google.com/p/vqmod/
Originally intended for OpenCart it basically allows virtual modifications of any php file using XML, and therefore leaving the original file untouched. There is a stand alone version that could be adapted to Joomla.
There are good and bad sides to this:
Bad - the final template or modification can rely on the original file being present, so if something like variable names change it could break, I suppose (not too up on this!)
Bad - if you want to move to a system where the site (or other) template is effectively a stand alone application, then modding rather than creating from scratch may not be the best way.
Bad - there is the potential for performance issues, though the guy who wrote the code has seen no issues.
Good - It really encourages leaving the core files untouched as there is no reason to touch them.
Good - in theory it makes any modification very lean as you do not end up with two unique version of the same file
Good - there is the potential of creating multiple virtual modifications of any one file allowing limitless possibilities.
The main down side with the system at the moment is that it is a bit of an expert orientated system in that you need to have a really good knowledge of the original file structure and use. Having said that, a more wizard base version might allow very quick modifications of files that could prove to be a huge advantage to less expert designers (like me!). For instance, this system would potentially replace many of the file overrides that are currently used in templates (com_content, modules and so on) very quickly and easily, especially where the modification is very simple (like changing the title tag).
Anyway, thought I would throw that into the mix.
Joss