My Favorite Design Apps:
There is no doubt TeX/LaTeX (universal) falls into this category. I use it to compose most of my documents.
Adobe Indesign CS2 (PPC) is also used a lot in layout design, with the facilitation of Adobe Photoshop (PPC).

My Favorite Office Apps:
Microsoft Word 2004 (PPC), although released from M$, is amazing good. I mainly use Microsoft Word 2004's notebook layout to record lectures and take lecture notes (this is like the Microsoft Onenote on Windows). I also like the tracking function in Word.
Most of the time, I rely on Apple's own Pages (universal) for writing papers and Keynote (universal) for creating amazingly beautiful presentation. I also use LaTeXit (universal) to create math equations to be incorporated into my slide shows.

My Favorite PDF Apps:
I use Mac OS X's own printing function to produce PDF files and Preview (universal) to read PDF files.
Occasionally, I would use Adobe Acrobat 7.0 (PPC) to do markup on PDF files.

My Favorite Web browser:
Safari (universal) is extremely fast and powerful. I use it 95% of the time. Sometimes I use Firefox (universal) and Opera (universal) to view websites like PConline, which is not well supported by Safari.

My Favorite Email App:
Thunderbird (PPC) is actually my favorite—it supports Duke's webmail system seemlessly, but it's not yet universal.
Currently, I use OS X's own Mail (universal). Although it doesn't support Duke's web mail that well, but there's hardly any problem; even if there is one, i can get around it. The advantage of Mail is smart folder and other handy nice functions.

My Favoite Chat Apps:
iChat (universal) is great! It's small, cute, and beautiful. It works with AIM and GoogleTalk seemlessly.
I also use Microsoft's dumn Messenger (PPC). Probably will get rid of it when I persuade all my friends to convert to AIM.

My Favorite Math Apps:
I use Mathematica (universal) to check my Calculus homework; it is now universal and runs fast.
My Favorite Digital-Life Apps:
iPhoto (universal) organizes my photo, and is used for creating albums and photo calenders.
iMovie (universal) leaves Windows Movie Maker in a dust. . . .
iTune (universal) leaves Windows Media Player in a dust. . . .
Photo Booth (universal) is used to take my pictures whenever I want to.
VLC (universal) is like Media Player Classic on Windows. Nice, nice, nice!!!

My Other Favorite Apps:
iGetter (PPC) is like FlashGet on Windows and works fairly well.
BitTorrent (PPC) is great for downloading special kinds of movies.
Automator (universal) is great for automating some of my work.
Address Book (universal) keeps records of my friends.
Comic Life (universal) is of great fun for creating comic books.
OnyX (universal) maintains Mac OS X in its nice shape.
Transmit (universal) is my favorite FTP app.
Disk Inventory X (PPC) displays your folder size in an intruging and beautiful layout.
Dictionary (universal) ensures that I'm never lost again in words. . . .
iAlertU (universal) protects my Mac from being stolen.
iCal (universal) makes sure I'm always on time.
DVD player (universal) plays DVD, high quality!!!
World of Warcraft (universal) is the best game on Mac.
Sherlock (universal) gives me access to AppleCare database.

Other apps I use:
iQQ (PPC), Font Book (universal), GarageBand (universal), iSerial Reader (PPC), iWeb (universal), LimeWire (PPC), Mactracker (PPC), Pacifist (universal), Quicktime (universal), RealPlayer (PPC), Skype (PPC), Stickies (universal), TextEdit (universal), TinkerTool (PPC), Toast Titanium (PPC), Windows Media Player (PPC).