What is the best way to release a closed source commercial app for Linux? What about adding entries to their application launcher of choice (ie kickstart menu on KDE or whatever)?

Firstly, don't try to force a Windows-centric view of software distribution onto a non_window platform. That's like a book publisher finding they have a monster hit of English literature and look to expand their market to South America and ask how they can get all those people to learn to read English so they will buy the book. It tends to be the wrong question.

Part of the problem stems from the misbelief that Linux is an operating system. It's not, it's a OS kernel. The think people think of as 'Linux' is actually the distribution like Red Hat, Fedora, Debian, Ubuntu, SuSE, and myriad others: they're the OSes. You don't target to 'Linux' you target to a distribution. Few distributions are truly compatible at the package or binary level. Following the book simile, the publisher now wants to translate the work into South American to improve sales. The next step will be to complain that there should a central authority in South America to dictate what language people speak and that it should look and sound like English, just like Jesus used in the Bible.

Anyway, there are two approaches to commercial distribution on Linux.

(1) Use the native package manager for your target distribution. You'll want to specify a limited set of distributions you target, and make debs/rpms available. Users download and install the software using their native package manager, and your software uses the local version of dependent libraries. The package managers take care of making sure dependencies are installed and configured correctly. You still need to test on all your supported platforms. This is generally the preferred method.

(2) Use the Macintosh approach of creating a standalone bundle of everything you need (all binaries, executables, assets, shared libraries, the works). You will still need to specify a limited set of distributions you target and make the bundles available for download. You will probably need to write a bespoke installer, or at least a custom wrapper, and integrate it into the OS. You will still need to test on all your supported platforms. This is the method Steam uses for its games.

You should follow the freedesktop.org standards for integrating your stuff into the launch system(s). See ColinDuquesnoy's reply above.

I'm preeety sure you can just get away with putting your stuff in /usr/share and /usr/bin. Then make a .desktop file so the application appears in the menu. It should work on most distros out there. Provide the regular .zip if the installer doesn't works on the user's *nix flavour.

I'm preeety sure you can just get away with putting your stuff in /usr/share and /usr/bin.

I would hunt you down and kill you if you did that. The contents of /usr are exclusively the province of my package manager, and if you go mucking around in there, you will break something.

Realistically, your two options are to either (a) integrate properly with my package manager, or (b) provide your software as a stand-alone zip/tar archive with no system dependencies.

I would hunt you down and kill you if you did that. The contents of /usr are exclusively the province of my package manager, and if you go mucking around in there, you will break something.

Installing into /opt currently seems like a rather reasonable approach since we currently need all files in the same directory. nixstaller seems pretty nice, but it bothers me somewhat that it hasn't really been updated since 2009. It also borders on the issue Bregma brought up, seems a bit like the Windows way of doing stuff.

It is the Windows way of doing stuff, but most people won't care. The purists will, but they'll either reject your product because it's not Free or they'll be really vehemently vocal in forums on the internet but can be safely ignored. The rest just want to install and use your software and don't care about such issues.

The real danger/disadvantage to having a complete bundle is (1) you will have to take care of your own security updates -- only really an issue if you have networked functionality or protect user assets in some way, and (b) if you have any external dependencies at all (eg. C or other language runtimes) your product could break on the next system upgrade. Unlike Windows, most Linux distros upgrade on a regular basis.

It really sounds like the single bundle is your best option. It does work well for Steam, although they have their own installer and automated update mechanism to alleviate the problems I outlined above. Have you considered going through Steam?