Here is a list of file changes that I found with the WSS SharePoint 2007 SP2 (I'll post some of the more interesting changes inside each of the files when I get some more time away from TechEd):
Template files:
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\SQL\STORE.SQL
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\SQL\STOREUP.SQL
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\SQL\SEARCHDB.SQL
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\SQL\SIGSTORE.SQL
C:\Program Files\Common Files\Microsoft Shared\web server
extensions\12\TEMPLATE\SiteTemplates\CENTRALADMIN\LISTS\DISTRIBUTIONLISTS\schema.xml
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\FEATURES\DocumentLibrary\DocLib\schema.xml
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\FEATURES\DiscussionsList\Discuss\schema.xml
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\SiteTemplates\Blog\Lists\Posts\schema.xml
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\SQL\SEARCHDBUPGRADE.SQL
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\GLOBAL\XML\ONET.XML
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\SQL\1033\SEARCHDBOOB.SQL
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\LAYOUTS\1033\OWS.JS
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\LAYOUTS\1033\FORM.JS
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\FEATURES\fields\fieldswss.xml
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\CONFIG\AdminResources\spadmin.resx
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\CONFIG\AdminResources\spadmin.en-US.resx
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\LAYOUTS\1033\BFORM.JS
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\LAYOUTS\qstnew.aspx
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\LAYOUTS\viewnew.aspx
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\LAYOUTS\FldNew.aspx
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\LAYOUTS\qstedit.aspx
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\LAYOUTS\viewedit.aspx
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\LAYOUTS\FldEdit.aspx
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\SQL\SIGSEARCHDB.SQL
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\GLOBAL\Lists\WEBTEMP\SCHEMA.XML
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\LAYOUTS\1033\CORE.JS
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\GLOBAL\Lists\WPLIB\SCHEMA.XML
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\XML\wss.xsd
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\LAYOUTS\1033\INIT.JS
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\SQL\CONFIGDB.SQL
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\XML\DeploymentManifest.xsd
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\CONFIG\TIMEZONE.XML
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\SQL\CONFIGUP.SQL
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\LAYOUTS\1033\IMGLIB.JS
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\1033\XML\RGNLSTNG.XML
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\LAYOUTS\ItemRWfAssoc.aspx
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\SQL\SIGCONFIGDB.SQL
C:\Program Files\Common Files\Microsoft Shared\Web Server Extensions\12\CONFIG\PreUpgradeCheck\WssPreUpgradeCheck.xml
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\IMAGES\ICODP.PNG
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\IMAGES\ICODS.PNG
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\IMAGES\ICODT.PNG
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\IMAGES\lg_ICODP.png
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\IMAGES\lg_ICODT.png
C:\Program Files\Microsoft Office Servers\12.0\Data\Config\noisecsy.txt
C:\Program Files\Microsoft Office Servers\12.0\Data\Config\tscsy.xml
Binary files:
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\ISAPI\Microsoft.SharePoint.dll
C:\Program Files\Common Files\Microsoft Shared\SERVER12\Server Setup Controller\WSSSETUP.DLL
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\ISAPI\OWSSVR.DLL
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\BIN\tquery.dll
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\BIN\mssrch.dll
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\BIN\ONETUTIL.DLL
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\BIN\STSWEL.DLL
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\ISAPI\Microsoft.SharePoint.Search.dll
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\BIN\offparser.dll
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\BIN\DBGHELP.DLL
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\BIN\psconfigui.exe
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\BIN\mssph.dll
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\CONFIG\BIN\Microsoft.SharePoint.ApplicationPages.dll
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\BIN\PSCONFIG.EXE
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\BIN\STSADM.EXE
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\BIN\bpa.userinterface.dll
C:\Program Files\Common Files\Microsoft Shared\SERVER12\Server Setup Controller\SETUP.EXE
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\BIN\onetnative.dll
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\CONFIG\BIN\STSSOAP.DLL
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\BIN\mssdmn.exe
C:\Program
Files\Common Files\Microsoft Shared\web server
extensions\12\CONFIG\ADMINBIN\Microsoft.SharePoint.ApplicationPages.Administration.dll
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\BIN\1033\mssmsg.dll
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\BIN\bpa.common.dll
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\ISAPI\microsoft.sharepoint.WorkflowActions.dll
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\BIN\mssearch.exe
C:\Program Files\Common Files\Microsoft Shared\Filters\xmlfilter.dll
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\BIN\PRESCAN.EXE
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\BIN\STSMMC.DLL
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\BIN\bpa.configcollector.dll
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\BIN\oleparser.dll
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\BIN\SPWRITER.EXE
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\BIN\wsstracing.exe
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\BIN\msscntrs.dll
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\BIN\query.dll
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\BIN\OWSTIMER.EXE
C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\BIN\custsat.dll
C:\Program Files\Common Files\Microsoft Shared\SERVER12\Server Setup Controller\WrapInst.exe
C:\Program Files\Common Files\Microsoft Shared\SERVER12\Server Setup Controller\WSS.en-us\WSETUPUI.DLL