I was previously using the top-voted answer, but it needs a bit of cleanup, so here it is redone for Xcode 4, with some improvements.
I've researched every file in this list, but several of them do not exist in Apple's official Xcode documentation, so I had to go on Apple mailing lists.
Apple continues to add undocumented files, potentially corrupting our live projects. This IMHO is unacceptable, and I've now started logging bugs against it each time they do so. I know they don't care, but maybe it'll shame one of them into treating developers more fairly.
If you need to customize, here's a gist you can fork: https://gist.github.com/3786883
#########################
# .gitignore file for Xcode4 and Xcode5 Source projects
#
# Apple bugs, waiting for Apple to fix/respond:
#
# 15564624 - what does the xccheckout file in Xcode5 do? Where's the documentation?
#
# Version 2.6
# For latest version, see: http://stackoverflow.com/questions/49478/git-ignore-file-for-xcode-projects
#
# 2015 updates:
# - Fixed typo in "xccheckout" line - thanks to @lyck for pointing it out!
# - Fixed the .idea optional ignore. Thanks to @hashier for pointing this out
# - Finally added "xccheckout" to the ignore. Apple still refuses to answer support requests about this, but in practice it seems you should ignore it.
# - minor tweaks from Jona and Coeur (slightly more precise xc* filtering/names)
# 2014 updates:
# - appended non-standard items DISABLED by default (uncomment if you use those tools)
# - removed the edit that an SO.com moderator made without bothering to ask me
# - researched CocoaPods .lock more carefully, thanks to Gokhan Celiker
# 2013 updates:
# - fixed the broken "save personal Schemes"
# - added line-by-line explanations for EVERYTHING (some were missing)
#
# NB: if you are storing "built" products, this WILL NOT WORK,
# and you should use a different .gitignore (or none at all)
# This file is for SOURCE projects, where there are many extra
# files that we want to exclude
#
#########################
#####
# OS X temporary files that should never be committed
#
# c.f. http://www.westwind.com/reference/os-x/invisibles.html
.DS_Store
# c.f. http://www.westwind.com/reference/os-x/invisibles.html
.Trashes
# c.f. http://www.westwind.com/reference/os-x/invisibles.html
*.swp
#
# *.lock - this is used and abused by many editors for many different things.
# For the main ones I use (e.g. Eclipse), it should be excluded
# from source-control, but YMMV.
# (lock files are usually local-only file-synchronization on the local FS that should NOT go in git)
# c.f. the "OPTIONAL" section at bottom though, for tool-specific variations!
#
# In particular, if you're using CocoaPods, you'll want to comment-out this line:
*.lock
#
# profile - REMOVED temporarily (on double-checking, I can't find it in OS X docs?)
#profile
####
# Xcode temporary files that should never be committed
#
# NB: NIB/XIB files still exist even on Storyboard projects, so we want this...
*~.nib
####
# Xcode build files -
#
# NB: slash on the end, so we only remove the FOLDER, not any files that were badly named "DerivedData"
DerivedData/
# NB: slash on the end, so we only remove the FOLDER, not any files that were badly named "build"
build/
#####
# Xcode private settings (window sizes, bookmarks, breakpoints, custom executables, smart groups)
#
# This is complicated:
#
# SOMETIMES you need to put this file in version control.
# Apple designed it poorly - if you use "custom executables", they are
# saved in this file.
# 99% of projects do NOT use those, so they do NOT want to version control this file.
# ..but if you're in the 1%, comment out the line "*.pbxuser"
# .pbxuser: http://lists.apple.com/archives/xcode-users/2004/Jan/msg00193.html
*.pbxuser
# .mode1v3: http://lists.apple.com/archives/xcode-users/2007/Oct/msg00465.html
*.mode1v3
# .mode2v3: http://lists.apple.com/archives/xcode-users/2007/Oct/msg00465.html
*.mode2v3
# .perspectivev3: http://stackoverflow.com/questions/5223297/xcode-projects-what-is-a-perspectivev3-file
*.perspectivev3
# NB: also, whitelist the default ones, some projects need to use these
!default.pbxuser
!default.mode1v3
!default.mode2v3
!default.perspectivev3
####
# Xcode 4 - semi-personal settings
#
# Apple Shared data that Apple put in the wrong folder
# c.f. http://stackoverflow.com/a/19260712/153422
# FROM ANSWER: Apple says "don't ignore it"
# FROM COMMENTS: Apple is wrong; Apple code is too buggy to trust; there are no known negative side-effects to ignoring Apple's unofficial advice and instead doing the thing that actively fixes bugs in Xcode
# Up to you, but ... current advice: ignore it.
*.xccheckout
#
#
# OPTION 1: ---------------------------------
# throw away ALL personal settings (including custom schemes!
# - unless they are "shared")
# As per build/ and DerivedData/, this ought to have a trailing slash
#
# NB: this is exclusive with OPTION 2 below
xcuserdata/
# OPTION 2: ---------------------------------
# get rid of ALL personal settings, but KEEP SOME OF THEM
# - NB: you must manually uncomment the bits you want to keep
#
# NB: this *requires* git v1.8.2 or above; you may need to upgrade to latest OS X,
# or manually install git over the top of the OS X version
# NB: this is exclusive with OPTION 1 above
#
#xcuserdata/**/*
# (requires option 2 above): Personal Schemes
#
#!xcuserdata/**/xcschemes/*
####
# Xcode 4 workspaces - more detailed
#
# Workspaces are important! They are a core feature of Xcode - don't exclude them :)
#
# Workspace layout is quite spammy. For reference:
#
# /(root)/
# /(project-name).xcodeproj/
# project.pbxproj
# /project.xcworkspace/
# contents.xcworkspacedata
# /xcuserdata/
# /(your name)/xcuserdatad/
# UserInterfaceState.xcuserstate
# /xcshareddata/
# /xcschemes/
# (shared scheme name).xcscheme
# /xcuserdata/
# /(your name)/xcuserdatad/
# (private scheme).xcscheme
# xcschememanagement.plist
#
#
####
# Xcode 4 - Deprecated classes
#
# Allegedly, if you manually "deprecate" your classes, they get moved here.
#
# We're using source-control, so this is a "feature" that we do not want!
*.moved-aside
####
# OPTIONAL: Some well-known tools that people use side-by-side with Xcode / iOS development
#
# NB: I'd rather not include these here, but gitignore's design is weak and doesn't allow
# modular gitignore: you have to put EVERYTHING in one file.
#
# COCOAPODS:
#
# c.f. http://guides.cocoapods.org/using/using-cocoapods.html#what-is-a-podfilelock
# c.f. http://guides.cocoapods.org/using/using-cocoapods.html#should-i-ignore-the-pods-directory-in-source-control
#
#!Podfile.lock
#
# RUBY:
#
# c.f. http://yehudakatz.com/2010/12/16/clarifying-the-roles-of-the-gemspec-and-gemfile/
#
#!Gemfile.lock
#
# IDEA:
#
# c.f. https://www.jetbrains.com/objc/help/managing-projects-under-version-control.html?search=workspace.xml
#
#.idea/workspace.xml
#
# TEXTMATE:
#
# -- UNVERIFIED: c.f. http://stackoverflow.com/a/50283/153422
#
#tm_build_errors
####
# UNKNOWN: recommended by others, but I can't discover what these files are
#
Best Answer
Is your Debug configuration's Base SDK set to a missing SDK? Xcode gets the specs for what flags the compiler supports from the configured base SDK. If it's missing, then Xcode doesn't know what compiler to show flags for.
Your Debug configuration might build correctly if you're using the Overview popup to set an override SDK. But since that's an override setting, the build setting inspector doesn't know about it. You have to set the base SDK to something valid, even if you're overriding it with the Active SDK popup.