Windows 3.1x/9x:
Windows 3.1 - Janus
Windows For Workgroups 3.1 - Kato, Sparta
Windows For Workgroups 3.11 - Snowball
Windows 95 - Chicago
Internet Explorer (first shipped in Microsoft Plus! for Windows 95) - O'Hare
Microsoft Plus! For Windows 95 - Frosting
Windows 95 OSR 2 - Detroit
Windows Desktop Update, Internet Explorer 4.0 (Windows 96) - Nashville
Windows 98 - Memphis
Windows 98 OEM/Corporate image cloning utility - Dolly
Windows Me - Millennium

Windows NT Family:
Windows NT 3.1 - NT OS/2
Windows NT 3.5 - Daytona
Windows NT 4.0 - Cairo
Microsoft Cluster Server - Wolfpack
Terminal Services, Windows Terminal Service - Hydra
Windows NT 4.0 Embedded - Impala
Windows 2000 - Memphis NT (i think this one could possibly be wrong.)
Windows 2000 Service Pack 1 - Asteroid
Windows 2000 64-bit - Janus
Neptune (Beta)
Odyssey (Never Released)
Windows XP - Whistler
Windows XP Embedded - Mantis
Windows XP Media Center Edition - eHome
Windows XP Media Center Edition 2003 - Freestyle
Windows XP Media Center Edition 2004 - Harmony
Windows XP Media Center Edition 2005 - Symphony
Windows Vista Media Center Edition - Diamond (this exists?)
Windows XP Service Pack 1 - Trainyard
Windows XP Service Pack 2 - Springboard
Windows XP Tablet PC Edition 2005 - Lone Star
Windows Server 2003 - Whistler Server
Windows Small Business Server 2003 - Bobcat
Windows Fundamentals for Legacy PCs - Eiger
Windows Vista - Longhorn
Windows Home Server - Quattro
Windows Small Business Server "Longhorn" - Cougar (unreleased?)
Windows Server 2008 - Longhorn Server
Hyper-V (Virtualization update for Windows Server 2008) - Viridian
Windows Essential Business Server - Centro
Windows 7 - Blackcomb/Vienna
Windows Media Center TV Pack 2008 - Fiji (never heard of this.)
Windows Azure (Windows cloud services platform) - Red Dog
Windows Embedded 2011 - Quebec
Windows Home Server 2010 - Vail

Windows CE:
Windows CE Family (Codename Pegasus)

Windows CE 1.0 - "Alder"
Platform builder - "Axe"
H/PC (HandHeld PC) Explorer - "Pegasus Explorer"

Windows CE 2.0 - "Adler" (Since, it was just an update)
Platform builder - "Axe" (again, it was just an update)
Windows CE 2.0 Sevices (Successor to H/PC Explorer) - "Minerva"
Handheld PC specification - "Mercury"
Palm-Size PC specification - "Gryphon"
Auto PC specification - "Apollo"

Windows CE 2.10 (Never released)- "Adler Echancement Pack"
Platform builder (Never released) - "Axe Enchancement Pack"

Windows CE 2.11 - "Birch"
Platform builder - "Buzzsaw"
Handheld PC specification - "Jupiter"
Palm-Size PC specification - "Orion" (1.1) "Wyvern" (1.2)
Webphone specification - "Hermes"
Auto PC Specification (Under the custom WinCE 2.12) - "GoldenEye"

Windows CE 3.0 - "Cedar"
Tools for developers - "Chainsaw"
ActiveSync 3.0 and 3.1 (Successor to Windows CE 2.0 Services) - "Xena"
Handheld PC specification - "Galileo"
PocketPC specification (successor of the PalmSize PCs) - "Rapier"
ActiveSync 3.1 and beyond - "Medusa"
Pocket PC 2002 specification - "Merlin"
Smartphone specification - "Stinger"

Until now, every WinCE OS codename was based on trees, and the development tools were based on tree-chopping utensils. Proposed codenames for Windows CE 4.0 were going to be DougFir (Douglas Fir) for the OS and "Dozer" (Bulldozer) for the tools. But the teams creating the new OS decided to change the codenames to names of whiskeys, so we have:

Windows CE 4.0 - "Talisker"

Windows CE 4.1 - "Jameson"

Windows CE 4.2 - "McKendrick"
Windows CE Mobile 2003 (stepstone between WinCE and WinMo) - "Ozone"

Windows CE 5.0 - "Macallan"

Windows Mobile 5.0 (dropped the WinCE designation) - "Magneto"

Windows Mobile 5.0 Second Edition - "Crossbow"

Windows Mobile 6.0 - "Yamasaki"
Windows Mobile Vista 6.0 [sic] - "Photon"

Windows Mobile 7.0 - "Photon"

thanks Commanderraf






Media Player Family:

DirectShow - Quartz
Windows Media Player - ActiveMovie Player
Windows Media Player 9 Series - Corona
Windows Media Player 11 For Windows XP - Polaris
Windows Media Player 11 For Windows Vista - Aurora


Visual Studio Family:

Visual Basic 1.0 - Thunder
Microsoft Visual C++ 4.1 - Zamboni
Microsoft Visual Basic 1.0 for MS-DOS - Escher
Visual Studio .NET 2002 - Rainier
Visual Studio .NET 2003 - Everett
ASP .NET Web Matrix - Saturn
ASP .NET Development Server - Cassini Web Server
Visual Web Developer Express Edition - Venus
Visual Studio 2005 - Whidbey
Visual Studio 2008 - Orcas
Roario (team system only release after Visual Studio 2008)
Visual Studio Team System - Burton
Visual Studio Team System's Source Control System - Hatteras
Visual Studio Team System Load Testing Suite - Ocracoke
Team Foundation Work Item Tracking - Currituck
Team Foundation Server SDK - Bodie
Visual Studio Team System's Designers For Architects - Whitehorse
Visual Studio 2005 Extensions for WinFX - Fidalgo
Online Version of Visual Studio - Tuscany
Phoenix(a microsoft research software development kit-
Hawaii(Microsoft Visual Studio 2010)
Camano (Test Case Management Client in VSTS 2010)

Exchange Server Family:

Exchange Server 4.0 - Spitfire, Touchdown
Exchange Server 5.5 - Osmium
Exchange Server 2000 - Platinum
Exchange Server 2003 - Titanium
Exchange Server 2007 - Exchange 12
Exchange Server 2010 - Exchange 14

SQL Server Family:

SQL Server 6.0 - SQL95
SQL Server Enterprise Manager - Startfighter
SQL Server 6.5 - Hydra
SQL Server 7.0 - Sphinx
SQL Server 7.0 OLAP Services - Plato
SQL Server 2000 (32-Bit) - Shiloh
SQL Server 2000 (64-Bit) - Liberty
SQL Server Reporting Services - Rosetta
SQL Server 2005 - Yukon
SQL Server 2005 Mobile Edition - Laguna
SQL Server 2008 - Katami / Akadia
SQL Report Designer 2.0 - Blue
SQL Server 2008R2 - Killimanjaro

Other Server Products:

Microsoft Proxy Server 1.0 - Catapuit

Experimental Operating Systems:

Singularity - Singularity
Midori (Microsoft Research Platform)

Expression Suite:

Expression Design - Acrylic
Expression Blend - Sparkle
Expression Web - Quartz

.NET

Microsoft .NET v1.0 - Lightning, Project 42
Microsoft .NET Framework v1.0 - COM+2.0, COM Object Runtime (COR), Universal Runtime (URT)
.NET Framework 3.0 - WinFX
Windows Presentation Foundation - Avalon
.NET My Services - HailStorm
Windows Communication Foundation - Indigo
Silverlight - Windows Presentation Foundation/Everywhere
Accelerator(allows developers to use managed code to program GPU's to create highly parallel programs)
ADO.NET Data Services - Astoria
Shared Source Common Language Infastructure - Rotor
Parallel Extensions to .NET Framework - ParallelFX
Microsoft Identity Framework - Zermatt

MSN/Windows Live:

Windows Live OneCare - A1
Blackbird(Online Content authoring technology developed alongside MSN 1.0 but cancelled in favor of HTML and ActiveX)
Windows Live Hotmail - Kahuna
Bing - Kumo
Windows Live Mail - Elroy
Microsoft Network, as shipped with Windwos 95 - Marvel
MSN Messenger Service - Tornado
Live Search - Rome

Xbox 360:

Blu-Ray 360 Player - Underwater (rumored)
XBL Cheater Scanning System - Blackwater (Unknown)
Xbox 360 Motherboard and Chipset - Falcon
Xbox 360 Screen Recording Software (XBox 360 SRS) - Nitrogen (existence is doubted)
NXE (New Xbox Experience) - Firebird
Xbox 360 Project "Helium" - Helium (a concept in which an Xbox 360 would be able to emulate Windows XP. was apparently scrapped since the release of Windows Vista)
Jasper (Fourth Hardware Revision with 65 nm CPU and 65nm GPU)
Opus (Revision of the Falcon motherboard but without an HDMI port. Used to replace Xenon motherboards during repairs)
Vailhalla - Future fith hardware revision with unifiired 65 nm CPU/GPU chip.
Xbox 360 Processor and codename - Xenon
Xbox 360 GPU and codename - Xenos
Xbox 360 Elite - Zephyr
Natal - Xbox 360 compatible gaming that uses 3D

Others:

Acroplis (Application framework for smart clients)
Aero Diamond (used during the development of Windows Vista to descripe the set of advanced user interface effects for the Desktop Window Manager to be introduced after Vista's release)
Microsoft Equipt - Albany
Zune Marketplace - Alexandria
Zune - Argo
ASP .NET Ajax - Atlas
Schedule+ 1.0 - Bandit
Microsoft Mail 3.0 - Bullet
Microsoft Office Communicator Web Access 2005 - Budapest


Captian, Slick - Early efforts to combine DOS and Windows, became "Jastro"
Jastro - "Non-Upgrade combined DOS/Windows setup" (Setup installs MS-DOS first and then Windows 3.1)
Windows 4.0 - Very early codename for Windows 95 (around 1990)
Jaguar - Chicago kernel
Cougar - 32bit protected mode kernel which runs on top of Jaguar
Cleveland - Planned successor of Chicago, became Nashville
ChiCairo - Early codename for Windows 98, when "Memphis NT" was still planned as a successor of Cairo
London - OLE-2 Based Shell and environment on top of Chicago (became Memphis later)
Tiger - Microsoft NetShow