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
I believe you are going to have to choose either jenkins or xcode server, not both. I don't know much about xcode server, but I do know about jenkins and xcode 5.
Builds with different configurations:
In the xcode plugin, you can set the scheme to use.
Automatic Build Number Increment
I added a parameter to my jenkins job called XCODEBUILDNUMBER. And whenever I start a build, I simply copy the build number out of my xcode project (I increment it manually. Mine looks like 080813A) and paste it into the XCODEBUILD parameter. I use this to name my output files, etc. There are plugins for jenkins that can automatically increment your build number, but they don't integrate, or sync with xcode.
Handling/synchronization of Build number between Jenkins & Apple CI
As I said before, I don't know of a way to sync the build numbers, but I just thought of a possible solution. You could use the command line tool plistbuddy, to set the build number in your info.plist, as a build step in your jenkins job.
Unit Tests
I have not successfully made unit tests work with Xcode5, but I know that the xcode plugin for jenkins supports it. I believe that the absence of the "Test After Build" key in the project settings may have something to do with it. If you make it work, i'd love to know. (I am also keen on making this work)
Acceptance Tests
From what I can tell, Frank is a command line tool. You can easily integrate it into your Jenkins job, and I believe that it will fail the build if your tests don't pass.
Accessing build products of the Apple CI from different Jenkins Jobs
Not completely sure what you mean, but with jenkins you can archive your build product (a .ipa), for later download and upload to a service like testflight. Again, I don't know much about Xcode Server (CI).
Backup of builds
As I said before, jenkins can archive your build product. Also, I use the the ${BUILD_NUMBER} variable in my build products directory, so I have a different directory for each build. This directory is also backed up to my Time Machine, and important builds copied to my web directory.
Automatic builds on git push to a specific branch
With the jenkins git plugin, you can make jenkins poll your scm in a interval specified by you, and can trigger a build on a change.
E-Mail notifications
I am sure that there is a plugin for this. (that emails you when a build failed/succeeded. in fact, this may be built-in)
In Closing
The xcode CI is a full independent CI, that may be hard to integrate with jenkins. Personally, I would recommend jenkins simply due to its extendability. Sorry I don't know much about Xcode Server.