The latest version of Sigil absolutely will merge .html or .xhtml files inside an EPUB container into 1 file. I have used it to edit poorly edited EPUBs where chapters are split across files. So I merge the two files then chapter break the big file at the end of the chapter I was working on. I don't know why you would want to, but you could merge every single .xhtml file into 1 giant file or just combine then resplit the chapters like I am doing.
Sigil comes in Linux, Mac and Windows flavors and it is GPL Open Source.
http://code.google.com/p/sigil/