I agree with Loren that the default arrangement (prior to 3.0) is the best aesthetically, but lately I find myself using the default apps — such as YouTube, Stocks, Weather, etc. — less and less.
After performing an ‘audition’—where in I leave the home screen blank until I need an app, then move it to the screen—this is the arrangement I currently have:
On the Dock: Messages is the most used app on the phone, Mail is great but I’d love a unified inbox, Tweetie is my favorite app (for any platform), and Camera so I never miss a shot.
Phone — I rarely use the Phone app, so it has traded places with the Messages app. Since it’s still a ‘mission critical’ app, I keep it in the top left corner, easily accessible.
Calendar — I sync with both MobileMe and my work Exchange Server, and mostly use the Month view.
Photos — default location, easy to find.
iPod — opposite corner of Phone, also critical-but-not-Dock-worthy.
Things — to keep me on task, syncs with the Mac version.
Notes — the perfect notepad for quick thoughts, meeting notes, etc.
Bible — The best Bible app for the iPhone, though I wish it were more fully-featured.
Clock — my alarm clock.
Deep Green — the best chess game for iPhone. Beautifully designed, terribly difficult to beat.
Words with Friends — Scrabble with friends (and strangers) at my leisure.
ScoreCenter — before ESPN released this app, the iPhone was incomplete. (I still wish there was a Weather-like scores app.)
Facebook — obligatory placement to remind me to actually try and care about Facebook.
CNN — great interface with nice local news features and live video.
Safari — best app on the iPhone.
TweetDeck — to keep pulse on trends, searches, and mentions (for @thecitychurch).
Settings — needs no explanation.