First some opinion, and then a list of what I use.
You will notice that for my information processing tools I hold dependability and flexibility above popularity. It is efficient to only learn something once. So I try to choose programs that are cross-platform, free, and adaptable.
I've watched computing trends move from reason-based toward fad-based. People are now often choosing to use what is fashionable, rather than what is good -- becoming good consumers, just as the industry would like them to be. I encourage everyone to give themselves some credit in assessing computing tools, and to comparison shop. There is a lot of good software that costs nothing, or just a little more.
The computer that is my workhorse both at work and at home is a NeXTstation turbo with monochrome monitor. Neither machine has crashed since 1991(as of 2003). The NeXTStep operating system was called by Byte Magazine "the most respected software on the planet". It is a crash-proof UNIX, is used by major financial houses, AT&T and the US Postal Service, and is the basis of Macintosh OS X. The 17" monochrome monitor is 91 pixels per inch versus the 72ppi PC standard. The screen runs with the same language as higher end printers (like ours) ... Postscript, thus allowing true WYSIWYG. The floppy drive automatically reads and writes NeXT, PC and Mac diskettes. I've never had to re-install my operating system to get out of a mess, never lost a .dll file and, like other UNIXes these are immune to all computer viruses. (Programs run in protected memory and cannot spread.)
The UNIX operating system is extremely modular and adaptable, which is why it has lasted since 1969. It forms the bulk of the infrastructure of the internet, and there are lots of free versions for almost every kind of computer hardware. UNIX creates an environment that makes it simple to "program with programs". What this means is that you have a "toolbox" of programs that do particular jobs really well, and you use them in combination to do the custom job at hand. The UNIX environment is designed to make this tool-use simple.
By way of analogy, note that you do things in the physical world with individual tools. You have a screwdriver (selectable bits), hammer, saw (various kinds), pencil, measuring tape, nails and screws, etc. You look at a job and decide what tools to use and in what steps to accomplish your task. In UNIX you do the same thing with info processing tools. For repetitive tasks it is easy to specify (in a script) the sequence of tools, and which next step to take given a particular condition, so all you need to say next time is "presto". This contrasts with the mega-package approach of buying a "door installation kit" for that task, which may not work for all doors, and which will leave you with all sorts of proprietary tools that are not much use for other things. (To make a table, you'd have to go out and buy "Microsoft Table" unless you had a handy set of tools and knew how to use them.)
The other machine on my desk at work is a Macintosh. Macs have run virtually the same OS since 1984, while other people worked through all the versions of DOS, Windows 3.1, Windows for Workgroups, Windows 95, and Windows 98, etc., etc., paying that Bill guy for every upgrade. Studies have always shown that the Mac has a lower Total Cost of Ownership than Wintel computers, even though the initial price of the latter may be lower. Here is an extensive recent study, complete with time budgets, that shows the advantage means big bucks in for-profit operations. Here is Apple's list of reasons for Mac versus Wintel. Sure it's biased, but I'm listing it because we IT guys would have time for more productive things if everyone ran Macs.
So why are Wintel (Windows/Intel) boxes so common? Marketing. Those are what most companies want to sell you. Only Apple sells Macs. Something like 80% of people who consider both Wintel and Mac buy Mac, but most people do not give themselves the credit to do the comparison shopping. People also fail to consider total cost of ownership, opting for the lowest initial outlay instead. Initial prices are now quite close.
The Zoology department is about 50:50 Mac:Wintel. We get a great many more problem calls about Wintel, and the latter problems are harder to fix. ZCU service is now configured so that people who choose high overhead systems will face high overhead -- we no longer offer free overhead reduction. (Don Brandys will help you for a fee.)
Steve Jobs was one of the 2 founders of Apple. The Macintosh was his vision (not shared by other Apple management at the time). Pixar (Toy Story, Bug's Life) is his, he founded NeXT, and is now back as CEO of Apple. I'd rather be rich like him than rich like that Bill guy. Sniff.
Linux is gaining huge popularity because it is free and more malleable and reliable than Windoze. But it's not the only free UNIX. FreeBSD is another good one to consider. FreeBSD is what we are running on the newest ZCU servers, just like Yahoo! and Hotmail. (Note that Hotmail is owned by Microsoft.)
GENERAL COMMENT: if it's not broken, don't fix it.
Corollary:
unless you *need* the additional features (or fixes) don't upgrade.
I prefer the question "how can I do this with my software?" to "can my software do this?", because often the answer to the latter question, after a whole lot of looking, is "No!". So I prefer programmable software. (Hence TeX and Splus.) We have all of this stuff at the Zoology Computing Unit.
more to come at some point. PRESENTATION/COMMUNICATION 50% of work of a scientist. Work on this part. Tufte's books. The Design Book for Non-Designers. Powerpoint really sucks: WiredPowerPointIsEvil.pdf