Here are a bunch of tweaks I apply to clean installs of OS Lion.
Bonus: Find out more tweaks at Blacktree's Secrets

Dock

  • Set default icon size

    defaults write com.apple.dock tilesize -float 48

  • Enable magnification

    defaults write com.apple.dock magnification -bool true

  • Set magnification icon size

    defaults write com.apple.dock largesize -float 96

  • Automatically hide and show the Dock

    defaults write com.apple.dock autohide -bool true

  • Display hidden applications as transulcent icons

    defaults write com.apple.dock showhidden -bool true

  • Show indicator lights for open applications

    defaults write com.apple.dock show-process-indicators -bool true

  • Enable highlight hover effect for the grid view of a stack

    defaults write com.apple.dock mouse-over-hilte-stack -bool true

  • Don't animate opening applications

    defaults write com.apple.dock launchanim -bool false

  • Don't animate mission control

    defaults write com.apple.dock expose-animation-duration -float 0

  • Enable spring loading for all Dock items (Demo)

    defaults write com.apple.dock enable-spring-load-actions-on-all-items -boolean true

Global Preferences

  • Disable "Reopen windows when logging back in"

    defaults write com.apple.loginwindow TALLogoutSavesState -bool false

  • Revert back to real "natural scrolling"

    defaults write NSGlobalDomain com.apple.swipescrolldirection -bool false

  • Enable full keyboard access for all controls (so you can navigate through the UI using keyboard)

    defaults write NSGlobalDomain AppleKeyboardUIMode -int 3

  • Enable subpixel font rendering on non-Apple LCDs

    defaults write NSGlobalDomain AppleFontSmoothing -int 2

  • Disable menu bar transparency

    defaults write NSGlobalDomain AppleEnableMenuBarTransparency -bool false

  • Always show scrollbars

    defaults write NSGlobalDomain AppleShowScrollBars -string "Always"

  • Show all filename extensions in Finder

    defaults write NSGlobalDomain AppleShowAllExtensions -bool true

  • Expand save panel by default

    defaults write NSGlobalDomain NSNavPanelExpandedStateForSaveMode -bool true

  • Expand print panel by default

    defaults write NSGlobalDomain PMPrintingExpandedStateForPrint -bool true

  • Disable auto-correct

    defaults write NSGlobalDomain NSAutomaticSpellingCorrectionEnabled -bool false

  • Disable window animations

    defaults write NSGlobalDomain NSAutomaticWindowAnimationsEnabled -bool false

  • Disable press-and-hold (character picker) for keys in favor of key repeat

    defaults write NSGlobalDomain ApplePressAndHoldEnabled -bool false

  • Set a blazingly fast keyboard repeat rate

    defaults write NSGlobalDomain KeyRepeat -int 0.02

  • Increase window resize speed for Cocoa applications

    defaults write NSGlobalDomain NSWindowResizeTime -float 0.001

  • Disable resume system-wide

    defaults write NSGlobalDomain NSQuitAlwaysKeepsWindows -bool false

  • Disable New Window animations

    defaults write NSGlobalDomain NSAutomaticWindowAnimationsEnabled -bool NO

Finder

  • Allow quitting Finder via ⌘ + Q (so will also hide desktop icons)

    defaults write com.apple.finder QuitMenuItem -bool true

  • Display full POSIX path as Finder window title

    defaults write com.apple.finder _FXShowPosixPathInTitle -bool true

  • Disable the warning when changing a file extension

    defaults write com.apple.finder FXEnableExtensionChangeWarning -bool false

  • Disable the warning before emptying the Trash

    defaults write com.apple.finder WarnOnEmptyTrash -bool false

  • Empty Trash securely by default

    defaults write com.apple.finder EmptyTrashSecurely -bool true

  • Use current directory as default search scope

    defaults write com.apple.finder FXDefaultSearchScope -string "SCcf"

  • Hide iDisk from the sidebar

    defaults write com.apple.finder RemoveIDiskFromSidebarOnStartup -bool true

  • Show Path bar

    defaults write com.apple.finder ShowPathbar -bool true

  • Show Status bar

    defaults write com.apple.finder ShowStatusBar -bool true

Disk Images (DMG)

  • Disable disk image verification

    defaults write com.apple.frameworks.diskimages skip-verify -bool true defaults write com.apple.frameworks.diskimages skip-verify-locked -bool true defaults write com.apple.frameworks.diskimages skip-verify-remote -bool true

  • Automatically open a new Finder window when a volume is mounted

    defaults write com.apple.frameworks.diskimages auto-open-ro-root -bool true defaults write com.apple.frameworks.diskimages auto-open-rw-root -bool true

Screensaver

  • Require password immediately after sleep or screen saver begins

    defaults write com.apple.screensaver askForPassword -int 1 defaults write com.apple.screensaver askForPasswordDelay -int 0

Safari

  • Disable Safari’s thumbnail cache for History and Top Sites

    defaults write com.apple.Safari DebugSnapshotsUpdatePolicy -int 2

  • Enable Safari’s debug menu

    defaults write com.apple.Safari IncludeInternalDebugMenu -bool true

  • Empty bookmarks bar

    defaults write com.apple.Safari ProxiesInBookmarksBar "()"

Terminal.app

  • Only use UTF-8 in Terminal.app

    defaults write com.apple.terminal StringEncodings -array 4

iTunes

  • Hide the Ping sidebar

    defaults write com.apple.iTunes disablePingSidebar -bool true

  • Disable all the other Ping stuff in iTunes

    defaults write com.apple.iTunes disablePing -bool true

Mail.app

  • Add invitations to iCal automatically

    defaults write com.apple.mail AddInvitationsToICalAutomatically -bool true

  • Display conversation messages in ascendent order

    defaults write com.apple.mail ConversationViewSortDescending -bool false

  • Show unred messages in bold

    defaults write com.apple.mail ShouldShowUnreadMessagesInBold -bool true

  • Display contact photos

    defaults write com.apple.mail EnableContactPhotos -bool true

  • Mark all conversation messages as read when opening a conversation

    defaults write com.apple.mail ConversationViewMarkAllAsRead -bool true

  • Do not display a summary of the body

    defaults write com.apple.mail NumberOfSnippetLines -int 0

  • Disable send and reply animations in Mail.app

    defaults write com.apple.mail DisableReplyAnimations -bool true defaults write com.apple.mail DisableSendAnimations -bool true

Misc

  • Disable crash reporter

    defaults write com.apple.CrashReporter DialogType -string "none"

  • Set computer name

    sudo /usr/sbin/networksetup -setcomputername 'Macbook Pro'

  • Allow only a single definition window when defining a word (``)

    defaults write com.apple.Dictionary ProhibitNewWindowForRequest -bool true

  • Disable the "Are you sure you want to open this application?" dialog

    defaults write com.apple.LaunchServices LSQuarantine -bool false

  • Enable AirDrop over Ethernet and on unsupported Macs running Lion

    defaults write com.apple.NetworkBrowser BrowseAllInterfaces -bool true

  • Disable window restore

    defaults write com.apple.Preview NSQuitAlwaysKeepsWindows -bool false

  • Avoid creating .DS_Store files on network volumes

    defaults write com.apple.desktopservices DSDontWriteNetworkStores -bool true

  • Disable Dashboard

    defaults write com.apple.dashboard mcx-disabled -boolean true

  • Show remaining battery time; hide percentage

    defaults write com.apple.menuextra.battery ShowPercent -string "NO" defaults write com.apple.menuextra.battery ShowTime -string "YES"

  • Disable local Time Machine backups

    hash tmutil &> /dev/null && sudo tmutil disablelocal

  • Enable Verbose boot

    sudo nvram boot-args="-v"

  • Show the ~/Library directory

    chflags nohidden ~/Library

  • Hide ~/bin directory

    chflags hidden ~/bin

  • Disable Spotlight

    sudo mdutil -a -i off

  • Disable disk journaling (recommended on SSD disks)

    diskutil disableJournal /Volumes/OSX

  • Disable Hibernation

    sudo pmset -a hibernatemode 0 sudo rm /var/vm/sleepimage

  • Reload affected applications

    for app in Safari Finder Dock Mail SystemUIServer; do killall "$app" >/dev/null 2>&1; done