TeXShop: Latex rulz. At least, whenever it's not driving you mad. If you don't work on a Mac, WinEdt may work for you.
Open Office: for compatibility with the rest of the world, and this one is free!
Adobe Indesign: this is just the thing for page layout design, but it is not cheap. You can try instead Scribus, which is totally free, multiplatform and has the most important features. Both generate PDF documents suitable for on-line publishing in, e.g. Issuu.
Paper writing tools
If you are cowriting a paper, Sharelatex might be better for you than your usual desktop suite.
Mendeley helps to organize PDFs and references for your articles. It has online and desktop clients. You can add notes to the papers online and outline key paragraphs too.
Stormboard provides a simple tool to organize ideas and arrange them in the proper order. Good for cooperative work as well.
I'm kind of partial myself to Adobe Photoshop, but it you need something good and free, go for Gimp.
To switch video formats, I usually dig MPEG StreamClip in my Mac, but I was very fond of Virtualdub on PC. Take your pick.
If you are working on PC and need to play mov videos, I'd go for Quicktime Alternative. It works faster than Quicktime and mess less with the system.
I'm sorry to say it, but I don't like iTunes just one bit. Too many limitations, too heavy for the computer and one has to be extra-careful with unwanted synchronizations. I've always been fond of Winamp, but the Mac version still needs some adjustments.
And, if you want to move things from and towards your iPod, you can always use (free) De-tune (for Mac only)
Grooveshark: Cloud music player, free (at the moment). My profile here, if you want to know what I'm listening lately
Dropbox: to keep your files synch-ed in all your computers
Dropbox Encore: to overcome the limination of one accound/one Dropbox folder (for Mac only)
And there's always Google Drive
Evernote: to share notes between Android mobile phones and computers
Settle Up: to quickly fix expenses when you go out with a group of people
CamScanner: if you need a PDF document out of a photo, quick and easy
Pocket: to keep a portable copy of a web page