I am very comfortable with OSX. Classic is forbidden on my machines. The only time I am using OS9 is when I wish to play some old pinball (but more on pinballs on their own page). Using OSX (since the public beta, although I converted definitely only with the arrival of Jaguar) I learned to eschew extreme customisation and excessive gadgets. OSX is not a toy but an efficient tool.
Here are the apps and utilities I am using
For scientific purposes I am using a TeX front end. Right now I prefer TeXshop but I may switch over to iTeXmac which has a better synchronisation. (Although Textures did finally appear, it was a major disappointment).
As far as the rest is concerned, and although I have a life license of MarinerWrite, I am not using any editor but TextEdit. This small app is a real gem. Since I have a iWork license at my lab I have also Pages but I never use it, unless I wish to open a .doc file with figures.
Finally a precious aid to those who are lazy is TypeIt4Me: once you have defined your shortcuts you'll find that typing is not a chore anymore.
For all analytical (and quite aften numerical also) computations I am using REDUCE. I really love this program: it performs the analytical calculations in the same way as human does and thus you do not need to issue constantly instructions. For my 2-D plots I am using Abscissa.
Another very handy small app (in fact not so small) is the RPN calculator. Among all the existing rpn calculators for the Mac, under OSX, only this one and the hp-emulator nonpareil pass the test with honours.
Finally Keynote has made possible for me to ignore apps from the dark side.
Intercal is the best calendar app around. I use DiskCatalogMaker for my catologuing needs. Since I own a Toast license at my lab I prefer this flexible app over the finder burn capabilities.
Pagespinner, Transmit and Mike's edge are my tools for web-page building and transferring. (Will Typestyler come out some day? I liked that app although by modern standards it is hopeless).
A great app for those who listen to music on their computer is Soundsource: it allows you to select your sound output with a single click.
Finally the two multi-tools I use from time to time are Onyx and ToolsX3.
As explained in the introduction I and not over-using customisation. My favourites are ClearDock, LabelsX and Windowshade, all based on the excellent Unsanity Application Enhancer. They are complmented by CanCombineIcons and CandyBar. A recent addition is MouseLocator made necessary by the ever increasing screen sizes.
I am very fond of contextual menus. The ones I constantly use are QuickImage and FinderIcon. I cross my fingers for a universal binary version to appear soon. Till they do, the only solution on an intel-based Mac is to use Pinki (a menu-bar item), as a replacement of the first and Micon (an application) as a replacement of the second.
AMVisibility is another favourite of mine together with QuickAccess. Finally another handy gui-related cmm is the DeskPicChange plugin.
I only use two mods in all my Macs: a Command-F mod which improves the behaviour of Spotlight and a french-modified keyboard which puts the dot back where it should have been (i.e. low-case at the numerical pad). Finally for my greek needs I use X-Greek which tries to do what Apple has for over twenty years refused to do: implement a greek OS.