I use BrewMath religiously to adjust decoction volumes and recalculate refractometer readings while brewing. BJCPStyles is convenient to have. It's searchable and nice to have for every reason you can think of.
BeerAlchemy is nice to have if you are a Mac user and have the Mac version of it. It's easier to use on the Mac than on an iPod/iPhone. I have used it at brewclub meetings to quickly throw together a recipe or just to play around with ingredients and ratios.
Simplenote is a free app that allows you to take notes. The neat thing is that the notes can be shared with another device or edited online. The iPod/iPhone syncs to all of the other devices. It allows the wife and I to both work on the weekly grocery list. The downside is that I often get sent out to do grocery shopping since I have the list on me at all times.
Enigmo is a neat game. Check it out.
They ported Doom over to the iPod/iPhone. The controls are obviously different, but the game is true to the way I remember it. Not a bad way to kill a few minutes during the day.
The Betty Crocker Cookbook app is nice. The iPad version is really nice, but the iPod/iPhone version is pretty good. It's something I can use while food shopping (see above, I am food shopping often).
There's also a really nice port of a HP 12C financial calculator. The interface looks like a 12C and all of the functions are there too. If you know how to use a 12C, this app is invaluable.