I am using the OS X system now for about 2 year. Before, I was for many many years on Linux (Debian), but the ongoing "tweaking" addiction was too time consuming. Once I started with my PhD I thought it might be a good idea to cut down on this this and focus on the real work ;)

My initial 2-3 month on OS X where not that great, considering that I was expecting a Linux with a nifty interface. Some things are just different, but after the initial hurdle I like the system today. A Unix which just works. Nice in a way.

Here is “my essential applications” list; some of them are OpenSource, some are commercial. Surely, OpenSource is a wonderful thing and I contribute to a few projects myself, but I am still willing to pay for good commercial applications!

System:

• MacPorts project (all the great stuff from the OpenSource world)
• Fink (too outdated, use MacPorts)
• Quicksilver (the most essential tool you need handy; connects with many apps)
• Jumpcut Clipboard Buffering (the name says it all, it is great)
• Growl (notification system inter-connecting with most apps)
• SimplyBurns (nice CD/DVD burning interface; better than onboard tools)
• SuperDuper (perfect backups, but I don’t use it since I have TimeMachine)
• Chicken of the VNC (only if you want to work remotely on other machines via VNC)
• Microsoft Remote Desktop Connection (RDC) (only if you want to work remotely on other MS machines)
• GrandPerspective (perfect for getting an idea of how HDD space is occupied)
• MenuMeters (great tool informing you about HDD, CPU, memory & network status)
• KeePassX and/or TrueCrypt (passwords to save ?)
• VMware Fusion (virtualisation)
• CoconutBattery (inspect the performance of you laptop battery)
• Font Book (inspect your installed fonts)
• Key Codes by Peter Maurer (find out about key mappings)
• pearScriptKeys (make you own global hot keys)
• TinkerTool System (various system level maintainance stuff)
• sshfs (transparently connects a remote files system via SSH to your machine, handy)
• ExpanDrive (faster and a bit more reliable than sshfs, but commercial)
• iDefrag (fragmented hard drive ? Use this tool. However, HFS+ hardly fragments in the first place :)
• LittleSnitch (personal firewall)
• RCDefaultApp (assign default applications for certain file types; System preferences)
• GnuPG & GPGMail (gpg mails & texts)
• MondoMouse (mouse super power – that’s what they claim)
• Tech Tool Deluxe (part of Apple Care Protection Plan)
• Rember (a frontend of memtest; unlike memtestosx free of charge)
• Spanning Sync
• Typinator
• Default Folder X (a must have!)
• ToggleHiddenFiles
• Name Mangler
• Service Scrubber
• Lab Tick
• MarcoPolo
• OpenTerminalHere

Work:

• Evernote, CircusPonies Notebook 3
• Bookends (reference management; Papers is a good alternative apparently)
• OmniGraffle (Awesome application for vector graphics, e.g. for making posters etc)
• Keynote (do you need to present your work, then this is for you)
• LaTeX packages, TexShop, LaTeX2rtf
• Mellel (great for technical and scholar writing; I use it for papers where LaTeX is over the top)
• OpenOffice 3.1 (horrible big beast, but at times you need to open Office documents)
• Skim (the very best pdf viewer ever)
• Apple Development Tools (essential if you do any development on your machine)
• Your favorite programming languages, myself Java, Perl and bit of Ruby & C++
• IntelliJ and Eclipse (both good IDEs for Java, I use the latter also for Perl & C++)
• TextMate, MacVim (my favourite text editors)
• MySQL, DbVisualizer (database stuff)
• R project (the ultimate free statistics environment)
• XMind
• AntiRSI (keeps you healthy – sort of)
• iFlash

Media:

• Adobe Photoshop CS3 (thankfully students get better rates :)
• Adobe Lightroom (great for working dynamically on RAW camera files)
• DNG Profile Editor
• iMovie HD (the old version 6 – forget about the new crippled iMovie versions)
• NeatImage PS plugin (get rid of noise in your pictures)
• Spyder3 Elite (do you need a calibrated monitor ? This set works well)
• HoudahGeo (geo tagging)
• RouteConverter 1.11 (converting various GPS files; only the old version works on Java 5)
• exiftool (A command-line interface to Image::ExifTool)
• Google Earth
• VLC (plays literally every media file)
• iShowU (screen cast program)
• Audacy (some audio work to do ? Record from the mic ?)
• ImageJ & API (nice if you do imaging with Java, used it in one of my science projects)
• Last.fm (the new form of radio these days ?)
• Comic Life (the need to draw a comic quickly ?)
• Incscape

Web stuff:

• Firefox, Camino, Opera & Safari
• Cyberduck (FTP & SSH; itegrates with Textmate)
• Paparazzi! (screenshots of a certain URL, can be handy)
• Skype (text, voip & video chat)
• GalleryRemote