I had a look at the functions generated by Flex and Bison. Neither of them can know whether the functions they generate will be called from other object files or not (and they don't provide a way to make them all static anyway). So I updated my script to automatically ignore these functions (and I attached the new version of the script).
With that and the help from Andrew Talbot we're down to less than 200 warnings :-) Getting there...
Here's the updated list.
dlls/cabinet/fdi.o: QTMupdatemodel should be made static dlls/cabinet/fdi.o: make_decode_table should be made static dlls/comctl32/tests/msg.o: flush_sequence should be made static dlls/dbghelp/storage.o: hash_table_find should be made static dlls/dmime/patterntrack.o: DMUSIC_CreateDirectMusicPatternTrackImpl should be made static dlls/dmime/tool.o: DMUSIC_CreateDirectMusicobjImpl should be made static dlls/dplayx/dplayx_global.o: DPLAYX_DestroyLobbyApplication should be made static dlls/dplayx/dplayx_global.o: DPLAYX_SetLocalSession should be made static dlls/dplayx/name_server.o: NS_GetOtherMagic should be made static dlls/dplayx/name_server.o: NS_SetRemoteComputerAsNameServer should be made static dlls/dplayx/dplay.o: cbDeleteGroupsElem should be made static dlls/dplayx/dplay.o: cbDeletePlayerElem should be made static dlls/dsound/capture.o: DirectSoundCaptureDevice_AddRef should be made static dlls/fusion/fusion.o: CompareAssemblyIdentity should be made static dlls/fusion/fusion.o: GetAssemblyIdentityFromFile should be made static dlls/fusion/assembly.o: assembly_get_architecture should be made static dlls/inetcomm/internettransport.o: InternetTransport_Read should be made static dlls/iphlpapi/ifenum.o: getInterfacePhysicalByName should be made static dlls/itss/chm_lib.o: chm_enumerate should be made static dlls/mountmgr.sys/mountmgr.o: DriverEntry should be made static dlls/msi/events.o: ControlEvent_UnSubscribeToEvent should be made static dlls/msi/string.o: msi_id2stringW should be made static dlls/msi/string.o: msi_strcmp should be made static dlls/msi/helpers.o: msi_ui_error should be made static dlls/msi/registry.o: msi_version_dword_to_str should be made static dlls/msi/helpers.o: reduce_to_shortfilename should be made static dlls/netapi32/nbnamecache.o: NBNameCacheUpdateNBName should be made static dlls/qcap/pin.o: IPinImpl_QueryInternalConnections should be made static dlls/riched20/string.o: ME_ConcatString should be made static dlls/riched20/style.o: ME_CopyToCF2W should be made static dlls/riched20/list.o: ME_DITypesEqual should be made static dlls/riched20/paint.o: ME_DrawParagraph should be made static dlls/riched20/list.o: ME_FindItemFwdOrHere should be made static dlls/riched20/row.o: ME_FindRowStart should be made static dlls/riched20/string.o: ME_GetOptimalBuffer should be made static dlls/riched20/para.o: ME_GetParaFormat should be made static dlls/riched20/paint.o: ME_GetYScrollVisible should be made static dlls/riched20/paint.o: ME_InvalidateFromOfs should be made static dlls/riched20/editor.o: ME_LinkNotify should be made static dlls/riched20/string.o: ME_MakeStringB should be made static dlls/riched20/para.o: ME_MarkForWrapping should be made static dlls/riched20/paint.o: ME_QueueInvalidateFromCursor should be made static dlls/riched20/paint.o: ME_Scroll should be made static dlls/riched20/para.o: ME_SetParaFormat should be made static dlls/riched20/style.o: ME_ToCFAny should be made static dlls/riched20/editor.o: REComboWndProc should be made static dlls/riched20/editor.o: REListWndProc should be made static dlls/riched20/reader.o: RTFExpandStyle should be made static dlls/riched20/reader.o: RTFGetClassCallback should be made static dlls/riched20/reader.o: RTFGetDestinationCallback should be made static dlls/riched20/reader.o: RTFGetInputName should be made static dlls/riched20/reader.o: RTFGetOutputName should be made static dlls/riched20/reader.o: RTFGetReadHook should be made static dlls/riched20/reader.o: RTFGetStyle should be made static dlls/riched20/reader.o: RTFHexToChar should be made static dlls/riched20/reader.o: RTFPeekToken should be made static dlls/riched20/reader.o: RTFSetClassCallback should be made static dlls/riched20/reader.o: RTFSetInputName should be made static dlls/riched20/reader.o: RTFSetOutputName should be made static dlls/riched20/reader.o: RTFSetToken should be made static dlls/riched20/reader.o: RTFUngetToken should be made static dlls/rpcrt4/rpc_message.o: NCA2RPC_STATUS should be made static dlls/rpcrt4/ndr_marshall.o: NdrByteCountPointerMemorySize should be made static dlls/rpcrt4/ndr_marshall.o: NdrRangeBufferSize should be made static dlls/rpcrt4/ndr_marshall.o: NdrRangeFree should be made static dlls/rpcrt4/ndr_marshall.o: NdrRangeMarshall should be made static dlls/rpcrt4/ndr_marshall.o: NdrRangeMemorySize should be made static dlls/rpcrt4/rpc_transport.o: RPCRT4_SpawnConnection should be made static dlls/rpcrt4/rpc_message.o: RPCRT4_ValidateCommonHeader should be made static dlls/rpcrt4/rpc_message.o: RPCRT4_receive_fragment should be made static dlls/rsaenh/handle.o: alloc_handle_table should be made static dlls/rsaenh/mpi.o: mp_2expt should be made static dlls/rsaenh/mpi.o: mp_abs should be made static dlls/rsaenh/mpi.o: mp_add_d should be made static dlls/rsaenh/mpi.o: mp_clamp should be made static dlls/rsaenh/mpi.o: mp_clear should be made static dlls/rsaenh/mpi.o: mp_cmp_mag should be made static dlls/rsaenh/mpi.o: mp_cnt_lsb should be made static dlls/rsaenh/mpi.o: mp_div should be made static dlls/rsaenh/mpi.o: mp_div_2 should be made static dlls/rsaenh/mpi.o: mp_div_2d should be made static dlls/rsaenh/mpi.o: mp_div_d should be made static dlls/rsaenh/mpi.o: mp_dr_reduce should be made static dlls/rsaenh/mpi.o: mp_dr_setup should be made static dlls/rsaenh/mpi.o: mp_exch should be made static dlls/rsaenh/mpi.o: mp_grow should be made static dlls/rsaenh/mpi.o: mp_init should be made static dlls/rsaenh/mpi.o: mp_init_size should be made static dlls/rsaenh/mpi.o: mp_lshd should be made static dlls/rsaenh/mpi.o: mp_mod_2d should be made static dlls/rsaenh/mpi.o: mp_mod_d should be made static dlls/rsaenh/mpi.o: mp_montgomery_calc_normalization should be made static dlls/rsaenh/mpi.o: mp_montgomery_reduce should be made static dlls/rsaenh/mpi.o: mp_montgomery_setup should be made static dlls/rsaenh/mpi.o: mp_mul_2 should be made static dlls/rsaenh/mpi.o: mp_mul_2d should be made static dlls/rsaenh/mpi.o: mp_mul_d should be made static dlls/rsaenh/mpi.o: mp_prime_is_divisible should be made static dlls/rsaenh/mpi.o: mp_prime_is_prime should be made static dlls/rsaenh/mpi.o: mp_prime_miller_rabin should be made static dlls/rsaenh/mpi.o: mp_reduce should be made static dlls/rsaenh/mpi.o: mp_reduce_2k should be made static dlls/rsaenh/mpi.o: mp_reduce_2k_setup should be made static dlls/rsaenh/mpi.o: mp_reduce_setup should be made static dlls/rsaenh/mpi.o: mp_rshd should be made static dlls/rsaenh/mpi.o: mp_set should be made static dlls/rsaenh/mpi.o: mp_signed_bin_size should be made static dlls/rsaenh/mpi.o: mp_sqr should be made static dlls/rsaenh/mpi.o: mp_sqrmod should be made static dlls/rsaenh/mpi.o: mp_zero should be made static dlls/rsaenh/handle.o: release_handle_table should be made static dlls/sane.ds/ds_ctrl.o: SANE_AutomaticCaptureDirectory should be made static dlls/sane.ds/ds_ctrl.o: SANE_FileSystemCopy should be made static dlls/sane.ds/ds_ctrl.o: SANE_PendingXfersStopFeeder should be made static dlls/sane.ds/ds_ctrl.o: SANE_SetupFileXfer2Get should be made static dlls/sane.ds/ds_ctrl.o: SANE_SetupFileXfer2GetDefault should be made static dlls/sane.ds/ds_ctrl.o: SANE_SetupFileXfer2Reset should be made static dlls/sane.ds/ds_ctrl.o: SANE_SetupFileXfer2Set should be made static dlls/setupapi/parser.o: PARSER_string_substW should be made static dlls/setupapi/virtcopy.o: VcpEnumFiles should be made static dlls/setupapi/virtcopy.o: VcpFlush16 should be made static dlls/setupapi/virtcopy.o: vsmStringCompare16 should be made static dlls/setupapi/virtcopy.o: vsmStringFind16 should be made static dlls/shell32/classes.o: HCR_GetDefaultIconFromGUIDW should be made static dlls/shell32/pidl.o: ILGetDisplayNameExA should be made static dlls/shell32/clipboard.o: RenderFILECONTENTS should be made static dlls/shell32/clipboard.o: RenderFILEDESCRIPTOR should be made static dlls/shell32/clipboard.o: RenderPREFEREDDROPEFFECT should be made static dlls/shell32/clipboard.o: RenderSHELLIDLISTOFFSET should be made static dlls/shell32/pidl.o: SHILCreateFromPathA should be made static dlls/shell32/trash.o: TRASH_DisposeElement should be made static dlls/shell32/xdg.o: XDG_GetPath should be made static dlls/shell32/pidl.o: _ILGetSTextPointer should be made static dlls/shell32/pidl.o: _ILGetTextPointerW should be made static dlls/urlmon/http.o: create_http_protocol should be made static dlls/user32/edit.o: EditWndProcW should be made static dlls/user32/cursoricon.o: LookupIconIdFromDirectory16 should be made static dlls/uxtheme/uxini.o: UXINI_ResetINI should be made static dlls/winealsa.drv/alsa.o: ALSA_PeekRingMessage should be made static dlls/winealsa.drv/waveout.o: wodSetVolume should be made static dlls/winedos/himem.o: DOSVM_AllocCodeUMB should be made static dlls/winedos/himem.o: DOSVM_AllocUMB should be made static dlls/winedos/int31.o: DPMI_FreeInternalRMCB should be made static dlls/wineps.drv/color.o: PSDRV_CmpColor should be made static dlls/wineps.drv/ps.o: PSDRV_WriteArrayGet should be made static dlls/wineps.drv/ps.o: PSDRV_WriteInitClip should be made static dlls/wineps.drv/ps.o: PSDRV_WriteRRectangle should be made static dlls/winex11.drv/graphics.o: X11DRV_SetupGCForPen should be made static dlls/winex11.drv/xvidmode.o: X11DRV_XF86VM_SetExclusiveMode should be made static dlls/winex11.drv/xrandr.o: X11DRV_XRandR_Cleanup should be made static dlls/winex11.drv/window.o: X11DRV_get_client_window should be made static dlls/winex11.drv/window.o: X11DRV_window_to_X_rect should be made static dlls/wininet/http.o: HTTP_FinishedReading should be made static dlls/wininet/http.o: HTTP_GetHeader should be made static dlls/wininet/http.o: HTTP_HttpOpenRequestW should be made static dlls/wininet/http.o: HTTP_HttpSendRequestW should be made static dlls/winmm/mci.o: MCI_DefYieldProc should be made static dlls/winmm/mci.o: MCI_GetDriverFromString should be made static dlls/winmm/mci.o: MCI_SendCommandFrom16 should be made static dlls/winmm/mci.o: MCI_SendCommandFrom32 should be made static dlls/winmm/mci.o: MCI_WriteString should be made static dlls/wintrust/asn.o: CRYPT_AsnEncodeInt should be made static dlls/wintrust/wintrust_main.o: WINTRUST_ReAlloc should be made static dlls/wnaspi32/winaspi16.o: ASPI_SendASPICommand should be made static dlls/wnaspi32/aspi.o: SCSI_GetDeviceName should be made static dlls/wuapi/updates.o: AutomaticUpdates_create should be made static programs/progman/dialog.o: DIALOG_Symbol should be made static programs/regedit/regproc.o: GetMultiByteStringN should be made static programs/regedit/childwnd.o: GetRootKeyName should be made static programs/regedit/regproc.o: GetWideStringN should be made static programs/regedit/hexedit.o: HexEdit_Unregister should be made static programs/regedit/regproc.o: processRegLinesA should be made static programs/regedit/regproc.o: processRegLinesW should be made static programs/taskmgr/taskmgr.o: Draw3dRect should be made static programs/taskmgr/taskmgr.o: Draw3dRect2 should be made static programs/taskmgr/taskmgr.o: FillSolidRect2 should be made static programs/taskmgr/graphctl.o: GraphCtrl_DrawPoint should be made static programs/taskmgr/graphctl.o: GraphCtrl_InvalidateCtrl should be made static programs/taskmgr/graphctl.o: GraphCtrl_Paint should be made static programs/taskmgr/graphctl.o: GraphCtrl_Resize should be made static programs/taskmgr/trayicon.o: TrayIcon_GetProcessorUsageIcon should be made static programs/taskmgr/applpage.o: UpdateApplicationListControlViewSetting should be made static programs/winecfg/winecfg.o: enumerate_valuesW should be made static programs/wineconsole/user.o: WCUSER_AreFontsEqual should be made static programs/wineconsole/wineconsole.o: WINECON_FetchCells should be made static programs/wineconsole/wineconsole.o: WINECON_GetHistoryMode should be made static programs/wineconsole/wineconsole.o: WINECON_SetHistoryMode should be made static programs/wineconsole/wineconsole.o: WINECON_SetHistorySize should be made static programs/winedbg/memory.o: be_cpu_build_addr should be made static programs/winedbg/memory.o: be_cpu_linearize should be made static programs/winedbg/winedbg.o: dbg_outputA should be made static programs/winedbg/debug.yy.o: lexeme_alloc should be made static programs/winedbg/dbg.tab.o: parser should be made static programs/winedbg/tgt_minidump.o: validate_file should be made static