BBEdit - every geek needs a great text editor, and exactly which one people use is a very personal choice, but that tends to display ones personal geek history. BBEdit pretty clearly marks me as 'old school Mac guy'. FWIW, I'm definitely a vi not an emacs guy, but have never felt inclined to use vi when I have the choice of an editor with a real GUI.
I find being able to edit files on remote servers directly via SFTP is something essential to my normal workflow.
iTerm - every geek needs terminal access. I prefer iTerm to the built in Terminal. Actually, iTerm 2.
Echofon - desktop twitter client of choice. I'm always surprised whenever I discover anyone that regularly uses twitter via the web interface. I've tried about half a dozen desktop twitter clients, and seem to have settled on Echofon for now. I use Tweetbot on the phone, I actually like that even more. I tweet from more than one account, so that is an important feature for me.
Google Chrome - Safari comes across as a bit bloated to me. I'm pretty bad at closing tabs, so Safari eats memory fast. I'll probably switch browsers back eventually, though, Safari has a few features I really like (like easily enabling me to open a PDF in a suitable other app). I also use Firefox.
Preview - I find myself looking at PDF docs all the time, for both work and hobbies. I seem to be using Skim - a PDF viewer designed for annotation etc - more and more, and it may well end up replacing Preview for most PDF docs.
Word - I've found working in Universities in which everyone uses Word makes it so much easier than alternatives, despite it not being my favourite word processor. So it is always open.
Scrivener - going to be my tool of choice for serious writing from now on, I think. This is an amazing tool for writing complicated documents, the sort of document I previously would have started in an outliner. Still a bit unsure about reference manager integration, but otherwise amazing.
Skype - I'm involved with at least a couple of groups that seem to have settled on Skype as a regular communications tool, particularly the Burning Man Australia crew and ICANN NCUC gang, plus some friends that use it as preferred IM, so I keep it open most of the time. I don't think I have used its video features ever, but I use both IM and voice chat regularly.
Mail - I finally made the big shift to Apple Mail. Now I've shifted, I'm unlikely to shift again for a really long time, unless someone designs a good IMAP mail client for people that receive massive amounts of mail on multiple mailing lists and multiple accounts and need to filter it all. At the moment, I'm also reading one email account through Sparrow as an experiment, but the rest are all through Mail. I'm experimenting with some add-ons, but not really satisfied.
Powerpoint - I lecture, and I like to lecture with slides, and that usually means Powerpoint. I prefer Keynote if I can, and I've used Prezi and think it is pretty cool, but Powerpoint is the bread and butter choice, because the machines I lecture on have Powerpoint installed, so it is just easier.