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 FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATESQLSTORE.SQL
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATESQLSTOREUP.SQL
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATESQLSEARCHDB.SQL
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATESQLSIGSTORE.SQL
C:Program FilesCommon FilesMicrosoft Sharedweb server
extensions12TEMPLATESiteTemplatesCENTRALADMINLISTSDISTRIBUTIONLISTSschema.xml
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATEFEATURESDocumentLibraryDocLibschema.xml
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATEFEATURESDiscussionsListDiscussschema.xml
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATESiteTemplatesBlogListsPostsschema.xml
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATESQLSEARCHDBUPGRADE.SQL
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATEGLOBALXMLONET.XML
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATESQL1033SEARCHDBOOB.SQL
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATELAYOUTS1033OWS.JS
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATELAYOUTS1033FORM.JS
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATEFEATURESfieldsfieldswss.xml
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12CONFIGAdminResourcesspadmin.resx
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12CONFIGAdminResourcesspadmin.en-US.resx
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATELAYOUTS1033BFORM.JS
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATELAYOUTSqstnew.aspx
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATELAYOUTSviewnew.aspx
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATELAYOUTSFldNew.aspx
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATELAYOUTSqstedit.aspx
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATELAYOUTSviewedit.aspx
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATELAYOUTSFldEdit.aspx
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATESQLSIGSEARCHDB.SQL
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATEGLOBALListsWEBTEMPSCHEMA.XML
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATELAYOUTS1033CORE.JS
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATEGLOBALListsWPLIBSCHEMA.XML
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATEXMLwss.xsd
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATELAYOUTS1033INIT.JS
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATESQLCONFIGDB.SQL
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATEXMLDeploymentManifest.xsd
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12CONFIGTIMEZONE.XML
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATESQLCONFIGUP.SQL
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATELAYOUTS1033IMGLIB.JS
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATE1033XMLRGNLSTNG.XML
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATELAYOUTSItemRWfAssoc.aspx
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATESQLSIGCONFIGDB.SQL
C:Program FilesCommon FilesMicrosoft SharedWeb Server Extensions12CONFIGPreUpgradeCheckWssPreUpgradeCheck.xml
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATEIMAGESICODP.PNG
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATEIMAGESICODS.PNG
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATEIMAGESICODT.PNG
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATEIMAGESlg_ICODP.png
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12TEMPLATEIMAGESlg_ICODT.png
C:Program FilesMicrosoft Office Servers12.0DataConfig
oisecsy.txt
C:Program FilesMicrosoft Office Servers12.0DataConfig scsy.xml
Binary files:
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12ISAPIMicrosoft.SharePoint.dll
C:Program FilesCommon FilesMicrosoft SharedSERVER12Server Setup ControllerWSSSETUP.DLL
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12ISAPIOWSSVR.DLL
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12BIN query.dll
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12BINmssrch.dll
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12BINONETUTIL.DLL
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12BINSTSWEL.DLL
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12ISAPIMicrosoft.SharePoint.Search.dll
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12BINoffparser.dll
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12BINDBGHELP.DLL
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12BINpsconfigui.exe
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12BINmssph.dll
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12CONFIGBINMicrosoft.SharePoint.ApplicationPages.dll
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12BINPSCONFIG.EXE
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12BINSTSADM.EXE
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12BINpa.userinterface.dll
C:Program FilesCommon FilesMicrosoft SharedSERVER12Server Setup ControllerSETUP.EXE
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12BINonetnative.dll
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12CONFIGBINSTSSOAP.DLL
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12BINmssdmn.exe
C:Program
FilesCommon FilesMicrosoft Sharedweb server
extensions12CONFIGADMINBINMicrosoft.SharePoint.ApplicationPages.Administration.dll
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12BIN1033mssmsg.dll
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12BINpa.common.dll
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12ISAPImicrosoft.sharepoint.WorkflowActions.dll
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12BINmssearch.exe
C:Program FilesCommon FilesMicrosoft SharedFiltersxmlfilter.dll
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12BINPRESCAN.EXE
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12BINSTSMMC.DLL
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12BINpa.configcollector.dll
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12BINoleparser.dll
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12BINSPWRITER.EXE
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12BINwsstracing.exe
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12BINmsscntrs.dll
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12BINquery.dll
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12BINOWSTIMER.EXE
C:Program FilesCommon FilesMicrosoft Sharedweb server extensions12BINcustsat.dll
C:Program FilesCommon FilesMicrosoft SharedSERVER12Server Setup ControllerWrapInst.exe
C:Program FilesCommon FilesMicrosoft SharedSERVER12Server Setup ControllerWSS.en-usWSETUPUI.DLL