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
#
These files contain user preference configurations that are in general specific to your machine, so it's better not to put it in SCM. Also, VS will change it almost every time you execute it, so it will always be marked by the SCM as 'changed'.
I don't include either, I'm in a project using VS for 2 years and had no problems doing that. The only minor annoyance is that the debug parameters (execution path, deployment target, etc.) are stored in one of those files (don't know which), so if you have a standard for them you won't be able to 'publish' it via SCM for other developers to have the entire development environment 'ready to use'.
Best Answer
I've struggled with this myself, and I can't tell you anything other than:
The first point is obvious enough. The second is to recognize that there's no getting around the fact that FLAs are binary blobs that hold all your visual assets and don't play well with versioning, but you can recognize the fact that some contents change frequently while others tend to be created once and then left alone. By dividing your assets into different FLAs, you can keep the large majority of changes into a small number of unstable FLAs, and the difference between stable and unstable content will be reflected in your versioned files.
Note that even if you can't load assets at runtime, compile-time sharing still lets you divide assets into an arbitrary number of FLAs. (Compile-time sharing is often overlooked - if you're not familiar with it, open a MovieClip's properties and check out the "Source" section at the bottom.) How to divide things will depend your project. The best I can suggest is to make divisions semantically - perhaps one FLA for each character, or one FLA for each section, or one FLA for each interface element, etc. As with all development the goal is to group related assets and eliminate duplication.
The third point is, since diffs are impossible, there's just no way around keeping a change document. My preferred way is to check the FLAs into versioning and note all changes in the check-in note, but the changes could also be in a separate document. (Note that it's vital that you keep the libraries in each FLA orderly, or someone reading the change description will have trouble finding the change.) However, since this can be a pain for some contents, it's also useful to designate certain FLAs as "unstable", and not bother with a change list. But if such files have a lot of dependencies on other files, you'll regret it later.
Unfortunately this is all I've discovered so far. Adobe has talked about changing to a text-based FLA format in a future version, but until that arrives, there's no easy solution.