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Hyper Estraier has a Google-like interface that has some additional features such as including regular expressions in your queries.

This is not an open source project. From data/textures/readme.txt:

(C) 2007-2009 Blood Frontier Team, all rights reserved.

The "textures" package included in Blood Frontier may only be distributed
with the Blood Frontier package. Redistribution or repacking outside
this context without the author's consent is strictly prohibited.

If you want a real open-source shooter that rocks, try Nexuiz.

EndNote does one thing [citation management] well. The problem is that citation management isn't a difficult thing to accomplish in software.

Absolutely true. Pybliographer has been available for years, so there is hardly a need for proprietary reference management software.

The security model of PHP is a nightmare, therefore it is a good thing that we now have a mature and free CMS written in Perl. If it had been available some time ago, I probably wouldn't have written my own.

I can relate a similar story about licensing issues with Matlab costing me time throughout my PhD. I am currently investigating Free Software alternatives (SciPy, and now Sage) for my post-doctoral employment.

You should also take a look at Octave, which is mostly Matlab-compatible.

But I use Mathematica because it is full of functionality, fairly reliable, and has a very elegant programming paradigm. Also, as a student, it'll cost me $100-150, depending on where I live, for the lifetime of my studentship, assuming no site license; the kinds of business that run this software commercially really don't care too much about a $2500 license fee.

Free software isn't about price -- it is about freedom. One of the research groups at my university cannot use Mathematica since a few weeks because the license expired, and neither renewing the license nor contacting tech support has so far brought a solution.

Another no-go is that Mathematica 6 notebooks are not compatible with Mathematica 5 notebooks. Also, the unwillingness of Wolfram to timely fix bugs leading to wrong results is unacceptable. I could go on ranting like this, but recently I have completely switched to Maxima and have not regretted it.

docs/license.txt:

It is only permissible to distrubute the game data(models, maps, textures, sound, etc) as a whole, and with the intention of being used with Alien Arena. It is not permissible to distribute individual portions or items of the game data without express consent from COR Entertainment. [...] Under no circumstances ALIEN ARENA 2007 as a whole be sold or used for profit, without express consent from COR Entertainment.

If you want a free-as-in-speech shooter that rocks, try Nexuiz.

AppArmor's main approach is somewhat less broad. It is more like putting certain applications into a MAC container to limit what an application can do, no matter who the user using the application is. A great example of this that most Slashdot readers should look into is putting the browser into a safety container.

Some time ago, I wrote a review of AppArmor, finding that it solves problems that don't exist. Looking at your browser example, the functionality provided by AppArmor can be implemented completely by setting up a different user and setting appropriate file ACLs.

For the real problems AppArmor provides little help. Can you confine network usage of a program, meaning your internal network cannot be accessed once your browser has been hacked? No. Can you limit the syscalls a program may use, reducing the risk of successful kernel exploits? No.

As long as it stays this way, I recommend to everyone to use SELinux, even though it is much more difficult to setup and configure.

The problems don't come from having NAT or a stateful firewall, but from using poorly designed protocols. There is hardly a justification for using more than one TCP or UDP port, or dynamically assigned destination ports.

For example, compare IPSec with OpenVPN: the former requires various UDP ports plus a completely new IP protocol, while the latter runs over a single UDP port. Now guess which one is much easier to get through a firewall.

I have only encountered two really useful extensions so far, the rest usually being too bloated or insecure to install them.

The first is the PrefBar, which allows to quickly change browser options.
For example, enable or disable Cookies, Java(Script) with a single click. Or choose from different proxies, which is very useful in combination with Tor.

For web developers, LiveHTTPHeaders is a must. It allows you to track redirects, view Cookies or view and manipulate POST requests.

I have only encountered two really useful extensions so far, the rest usually being too bloated or insecure to install them.

The first is the PrefBar, which allows to quickly change browser options.
For example, enable or disable Cookies, Java(Script) with a single click. Or choose from different proxies, which is very useful in combination with Tor.

For web developers, LiveHTTPHeaders is a must. It allows you to track redirects, view Cookies or view and manipulate POST requests.