The build in TextEdit is particularly good, fast and powerful for simple tasks, and I am fond of using the plain text mode (Shift + Command + T) for fast access. However, we use LaTeX for scientific writing, aren't we? The LaTeX editor on mac is called TexShop freeware, but that is just the editor. You should also install TexLive system, for example MacTex freeware. The installation is staightforward, and if you need extra packages, use i-Installer freeware.
After installing the Tex system, if you just want to generate a quick snippet of a very short tex image, for example, equation/table for your presentation, you should use LaTeXiT freeware. Great things on a mac: drag and drop works almost everywhere! For orgnizing references, you can defintely use your favarite text editor to work with plain .bib file, or try BibDesk freeware for a graphical approach. I only give BibDesk 3 stars, not because it is bad, but you don't really need to use it - you have Papers shareware to organize your papers, and simply clicking all relavent papers, and exporting it to a .bib file save you a lot of time. I rarely give a non-free software 5 stars, but it is really worthy evey penny you spend, abeilt expensive (there is student discount, not faculty discount though). At least you should give it a try. Talking about the refernce tools, if you are still using "old style" microsoft word writing your paper (or communicate with your collaborators with word documents), you should try Bookends shareware, saving your time but not cheap neither. As a note, Papers can export files to many different reference styles, including EndNote XML, BibTeX library, PDF etc.
Microsoft Office Suite commercial is also available on mac. Word is comparable to Pages in Apple's iWork Suite commercial, and Pages is easier to use for creating fancy posters. Excel is way more powerful than Numbers in iWork, but Numbers is still an interesting approach. However, PowerPoint is way behind iWork's KeyNote in iWork. A very useful plugin for Keynote is LinkBack: you can use LaTeXiT to generate equations and drag it to your Keynote slides, and later click on the image link back to LaTeXiT to modify the equation. The open source couterparts OpenOffice Aqua freeware and NeoOffice have a long way to catch up (but usable), while Google Docs Suite freeware lacks features but easy for collaborating and sharing. One line summarize: considering both features and prices, iWork wins.
For programming or general purpose, both vi/vim and emacs have a lot of editors, but I don't have much experience with them. For example, you can try Aquamacs Emacs, or Carbon Emacs. There is also an instruction for setting up Emacs Speaks for Statistics (ESS) with Enhanced Carbon Emacs plugin. Notice that you need to install X11 for displaying R graphics if it is not alreay on your system, you can find it on the Leopard installation disk. Besides the standard R you can download from CRAN or the developer page, you can also try Java GUI for R (JGR) for interactive plots (very good for teaching EDA type course), which is deveoped by a group at AT&T. Matlab users also get mac support, but I never tried to run it on my ancient powerbook G4. In addition, the optional Xcode on Leopard should be great for software developers, or writing codes, but there is a bit of learning curve, and I still need time to explore this application.
On the otherside, Textmate shareware is great for programmers, very powerful once you know how to use it. Great editor software to own if you are going to use it a lot. If you want a free alternative, try TextWrangler freeware, and if you are happy with it, you might want to try its commertial version BBEdit shareare. Eclipse is free for Java developers, and here is the instruction to install Java and the IDE. Because I don't use Java much, so I won't comment on it right now.
For a simple HTML editor to write your website, try Taco HTML Edit freeware. And if you want an advanced Cascade Style Sheets (CSS) editor, there is the CSSEdit shareware. Or if you don't want to build your website from scratch, you should try iWeb free with every new mac. iWeb is beautiful and easy to use, but not so much customization, so I don't quite like it. Alternatively, RapidWeaver shareware as another template based web creation application is much more powerful, but not free. As a Googler, I had to advertise Google Sites freeware, but admit it feature lacking. I created my STA 103 course website using RapidWeaver and Google Docs. Recently, there is also lots of publication on Coda, but I have never used it.
Last not the least, if you like to write journals on a computer, try WriteRoom shareware. It reminds me the days I kept my life journals on a black screen BBS.
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