Well there used to be a cygwin-based version of isomaster here, but due to recent discoveries by myself, this is no longer necessary.
The best free ISO editor would probably be the giveaway version of UltraISO, which you can find here: http://www.raymond.cc/forum/freebies/12282-free-ultraiso-v9-full-license-key.html
If UltraISO's not enough to get the job done, there's always other free tools as well.
Totalmounter is a really good virtual drive app, with features never seen before: http://www.kernsafe.com/product/totalmounter.aspx
Imdisk is a pretty cool virtual drive program, which has one really cool feature which I've used before, remote mounting of image files and physical drives: www.ltr-data.se/opencode.html
You can then use the virtual drive as a source for UltraISO to create a new compilation.
There's also Imgburn, an excellent cd burning and creation suite: http://www.imgburn.com/
And last but not least, mkisofs, originally a unix-based iso filesystem creator: http://code.google.com/p/mkisofs-md5
Note: The link listed above will be the best one once it is updated to v3 of cdrtools.
Until then I prefer using this version of mkisofs: http://opensourcepack.blogspot.com/2011/11/cdrtools-mingw-binary.html
I really do wish there was a good opensource / freeware ISO editing app, but it doesn't look like there will be one anytime soon...