ROM Hack ROM "Dissection"

[Deleted member 310901]

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[FAST6191]

There many game specific tools but many of those will probably want mono or wine if they work at all. As for linux proper (and I guess mac for that matter) there are ports of ndstool to a native linux binary
http://codinglab.blogspot.co.uk/2007/07/nintendo-ds-homebrew-under-linux-ubuntu.html

Surprisingly java is not that popular for ROM hacking tools (I am as shocked as anybody although I don't much care for Java so that is OK) but you could try http://llref.emutalk.net/projects/ctool/

Compression in java
http://dsdecmp.googlecode.com/svn/trunk/Java/

There are a few open source projects as well that might compile across and some people are trying things with python as well.

If you are not wanting to do wine or mono (or a VM but that probably defeats the point) you will probably find most of rom hacking quite hard to pull off. I did have a ROM hacking on linux set of links somewhere although the above is pretty much the big stuff.