This is something that i've been meaning to test for a longtime and have eventually gotten around to it.It might be of interest to others...
A tester is directly connected to fa0/1 on a 3550.
interface FastEthernet0/1
switchport trunk encapsulation dot1q
switchport mode trunk
no keepalive
speed 100
duplex full
Switch1#sh int fa0/1 switchport
Name: Fa0/1
Switchport: Enabled
Administrative Mode: trunk
Operational Mode: trunk
Administrative Trunking Encapsulation: dot1q
Operational Trunking Encapsulation: dot1q
Negotiation of Trunking: On
Access Mode VLAN: 10 (VLAN0010)
Trunking Native Mode VLAN: 1 (default)
Administrative Native VLAN tagging: enabled
Voice VLAN: none
Administrative private-vlan host-association: none
Administrative private-vlan mapping: none
Administrative private-vlan trunk native VLAN: none
Administrative private-vlan trunk Native VLAN tagging: enabled
Administrative private-vlan trunk encapsulation: dot1q
Administrative private-vlan trunk normal VLANs: none
Administrative private-vlan trunk associations: none
Administrative private-vlan trunk mappings: none
Operational private-vlan: none
Trunking VLANs Enabled: ALL
Pruning VLANs Enabled: 2-1001
Capture Mode Disabled
Capture VLANs Allowed: ALL
Protected: false
Unknown unicast blocked: disabled
Unknown multicast blocked: disabled
Appliance trust: none
I've captured the different frames arriving on the tester with the default native vlan 1.
PVST+ BPDU
R1(PKTS:4 of 7)#sh 5
=============================================================================
01:15:10.967 UTC Fri Mar 1 2002 Relative Time: 3.631786
Packet 5 of 7 In: FastEthernet0/0
Ethernet Packet: 64 bytes
Dest Addr: 0100.0CCC.CCCD, Source Addr: 0013.8081.C801
IEEE 802.3 length: 50
LLC DSAP: 0xAA, SSAP: 0xAA, Control: 0x03
SNAP OUI: 0x00000C, Protocol: 0x010B
Data:
0 : 0000 0000 0060 0100 1380 81C8 0000 0000 0060 0100 .....`...........`..
20 : 1380 81C8 0080 0100 0014 0002 000F 0000 0000 0002 ....................
40 : 0001 ..
IEEE BPDU
R1(PKTS:4 of

#sh 5
=============================================================================
00:49:22.935 UTC Fri Mar 1 2002 Relative Time: 0.767894
Packet 5 of 8 In: FastEthernet0/0
Ethernet Packet: 60 bytes
Dest Addr: 0180.C200.0000, Source Addr: 0013.8081.C801
IEEE 802.3 length: 38
LLC DSAP: 0x42, SSAP: 0x42, Control: 0x03
IEEE SPANNING TREE Protocol ID: 0x0000, Version: 0x00
Type: 0x00, Flags: 0x00
Root ID: 6001 0013.8081.C800, Root Path Cost: 0x00000000
Bridge ID: 6001 0013.8081.C800, Port ID: 0x8001
Message Age: 0.0, Max Age: 20.0, Hello Time: 2.0, Forward Delay: 15.0
CDP
R1(PKTS:1 of 3)#sh 1
=============================================================================
00:06:51.179 UTC Fri Mar 1 2002 Relative Time: 24.395975
Packet 1 of 3 In: FastEthernet0/0
Ethernet Packet: 387 bytes
Dest Addr: 0100.0CCC.CCCC, Source Addr: 0013.8081.C801
IEEE 802.3 length: 373
LLC DSAP: 0xAA, SSAP: 0xAA, Control: 0x03
SNAP OUI: 0x00000C, Protocol: 0x2000
CDP Cisco Discovery Protocol
Version: 0x02, Time to Live: 0xB4, Checksum: 0xCED5 (OK)
Device ID: Switch1
Version: Cisco IOS Software, C3550 Software (C3550-IPSERVICES-M), Version 12.2(44)SE5, RELEASE SOFTWARE (fc2)
Copyright (c) 1986-2009 by Cisco Systems, Inc.
Compiled Thu 22-Jan-09 02:50 by gereddy
Platform: Cisco WS-C3550-24-PWR
Addresses: 0
Port ID: FastEthernet0/1
Capabilities:
Switch (Level 2 switching).
IGMP conditional filtering.
Protocol-Hello: OUI: 0x00000C, Protocol-ID: 0x0112
Addn'l data: 0000 0000 FFFF FFFF 0102 21FF 0000 0000 0000 0013 8081 C800 FF00 00
VTP Management Domain: cisco
Native VLAN: 10
Duplex Mode: full
Extended Trust: 0 (NO Extended Trust)
COS for Untrusted Ports: 0
Management-Addresses: 1
IP: 0.0.0.0
Power Available: Request-ID: 0, Power-Management-ID: 1
Available-Power: 0, Management-Power-Level: -1
DTP
R1(PKTS:1 of 3)#sh 2
=============================================================================
00:06:57.575 UTC Fri Mar 1 2002 Relative Time: 30.791975
Packet 2 of 3 In: FastEthernet0/0
Ethernet Packet: 60 bytes
Dest Addr: 0100.0CCC.CCCC, Source Addr: 0013.8081.C801
IEEE 802.3 length: 39
LLC DSAP: 0xAA, SSAP: 0xAA, Control: 0x03
SNAP OUI: 0x00000C, Protocol: 0x2004
Data:
0 : 0100 0100 0A63 6973 636F 0000 0200 0581 0003 0005 .....cisco..........
20 : A500 0400 0A00 1380 81C8 0100 0000 0000 0000 ..................
VTP
R1(PKTS:1 of 2)#sh 3
=============================================================================
00:17:19.183 UTC Fri Mar 1 2002 Relative Time: 13.631967
Packet 2 of 2 In: FastEthernet0/0
Ethernet Packet: 99 bytes
Dest Addr: 0100.0CCC.CCCC, Source Addr: 0013.8081.C801
IEEE 802.3 length: 85
LLC DSAP: 0xAA, SSAP: 0xAA, Control: 0x03
SNAP OUI: 0x00000C, Protocol: 0x2003
Data:
0 : 0101 0105 6369 7363 6F00 0000 0000 0000 0000 0000 ....cisco...........
20 : 0000 0000 0000 0000 0000 0000 0000 0000 0000 0000 ....................
40 : 0000 0000 3933 3033 3031 3031 3131 3038 DB65 5893 ....930301011108.eX.
60 : 3E6F 2B19 CE7D 84E5 76FA 4C68 0101 0002 00 .o+..}..v.Lh.....
Next, ive modified the native vlan id from its default 1 to 100
Switch1#sh runn int fa0/1
Building configuration...
Current configuration : 193 bytes
!
interface FastEthernet0/1
switchport access vlan 10
switchport trunk encapsulation dot1q
switchport trunk native vlan 100
switchport mode trunk
no keepalive
speed 100
duplex full
end
PVST+ BPDU
R1(PKTS:1 of

#sh 2
=============================================================================
01:10:34.979 UTC Fri Mar 1 2002 Relative Time: 1.144112
Packet 2 of 8 In: FastEthernet0/0
Ethernet Packet: 68 bytes
Dest Addr: 0100.0CCC.CCCD, Source Addr: 0013.8081.C801
DOT1Q Tag ID: 0x8100, Priority: 7, CFI: 0, VLAN ID: 1
Protocol: 0x0032
Data:
0 : AAAA 0300 000C 010B 0000 0000 0060 0100 1380 81C8 .............`......
20 : 0000 0000 0060 0100 1380 81C8 0080 0100 0014 0002 .....`..............
40 : 000F 0000 0000 0002 0001 ..........
IEEE BPDU
R1(CAPTURE:6)#sh 1
=============================================================================
01:10:34.979 UTC Fri Mar 1 2002 Relative Time: 1.144071
Packet 1 of 8 In: FastEthernet0/0
Ethernet Packet: 60 bytes
Dest Addr: 0180.C200.0000, Source Addr: 0013.8081.C801
IEEE 802.3 length: 38
LLC DSAP: 0x42, SSAP: 0x42, Control: 0x03
IEEE SPANNING TREE Protocol ID: 0x0000, Version: 0x00
Type: 0x00, Flags: 0x00
Root ID: 6001 0013.8081.C800, Root Path Cost: 0x00000000
Bridge ID: 6001 0013.8081.C800, Port ID: 0x8001
Message Age: 0.0, Max Age: 20.0, Hello Time: 2.0, Forward Delay: 15.0
VTP
R1(CAPTURE:1)#sh 1
=============================================================================
00:32:36.879 UTC Fri Mar 1 2002 Relative Time: 12.136013
Packet 2 of 2 In: FastEthernet0/0
Ethernet Packet: 354 bytes
Dest Addr: 0100.0CCC.CCCC, Source Addr: 0013.8081.C801
DOT1Q Tag ID: 0x8100, Priority: 0, CFI: 0, VLAN ID: 1
Protocol: 0x0150
Data:
0 : AAAA 0300 000C 2003 0102 0102 4564 0000 0000 0000 ...... .....Ed......
20 : 0000 0000 0000 0000 0000 0000 0000 0000 0000 0000 ....................
40 : 0000 0000 0000 0000 1400 0107 0001 05DC 0001 86A1 ....................
60 : 6465 6661 756C 7400 1400 0108 0002 05DC 0001 86A2 default.............
80 : 564C 414E 3030 3032 1400 0108 000A 05DC 0001 86AA VLAN0002............
100 : 564C 414E 3030 3130 1400 0108 0064 05DC 0001 8704 VLAN0010.....d......
120 : 564C 414E 3031 3030 1400 0108 00C8 05DC 0001 8768 VLAN0100...........h
140 : 564C 414E 3032 3030 1800 0109 0190 05DC 0001 8830 VLAN0200...........0
160 : 766F 6970 5F76 6C61 6E00 0000 1400 0108 0258 05DC voip_vlan........X..
180 : 0001 88F8 564C 414E 3036 3030 2000 020C 03EA 05DC ....VLAN0600 .......
200 : 0001 8A8A 6664 6469 2D64 6566 6175 6C74 0101 0000 ....fddi-default....
220 : 0401 0000 2800 0312 03EB 05DC 0001 8A8B 746F 6B65 ....(...........toke
240 : 6E2D 7269 6E67 2D64 6566 6175 6C74 0000 0101 0000 n-ring-default......
260 : 0401 0000 2400 040F 03EC 05DC 0001 8A8C 6664 6469 ....$...........fddi
280 : 6E65 742D 6465 6661 756C 7400 0201 0000 0301 0001 net-default.........
300 : 2400 050D 03ED 05DC 0001 8A8D 7472 6E65 742D 6465 $...........trnet-de
320 : 6661 756C 7400 0000 0201 0000 0301 0002 fault...........
CDP
R1(CAPTURE:2)#sh 2
=============================================================================
00:39:58.391 UTC Fri Mar 1 2002 Relative Time: 27.315961
Packet 2 of 2 In: FastEthernet0/0
Ethernet Packet: 388 bytes
Dest Addr: 0100.0CCC.CCCC, Source Addr: 0013.8081.C801
DOT1Q Tag ID: 0x8100, Priority: 7, CFI: 0, VLAN ID: 1
Protocol: 0x0172
Data:
0 : AAAA 0300 000C 2000 02B4 CBE9 0001 000B 5377 6974 ...... .........Swit
20 : 6368 3100 0500 BF43 6973 636F 2049 4F53 2053 6F66 ch1....Cisco IOS Sof
40 : 7477 6172 652C 2043 3335 3530 2053 6F66 7477 6172 tware, C3550 Softwar
60 : 6520 2843 3335 3530 2D49 5053 4552 5649 4345 532D e (C3550-IPSERVICES-
80 : 4D29 2C20 5665 7273 696F 6E20 3132 2E32 2834 3429 M), Version 12.2(44)
100 : 5345 352C 2052 454C 4541 5345 2053 4F46 5457 4152 SE5, RELEASE SOFTWAR
120 : 4520 2866 6332 290A 436F 7079 7269 6768 7420 2863 E (fc2).Copyright (c
140 : 2920 3139 3836 2D32 3030 3920 6279 2043 6973 636F ) 1986-2009 by Cisco
160 : 2053 7973 7465 6D73 2C20 496E 632E 0A43 6F6D 7069 Systems, Inc..Compi
180 : 6C65 6420 5468 7520 3232 2D4A 616E 2D30 3920 3032 led Thu 22-Jan-09 02
200 : 3A35 3020 6279 2067 6572 6564 6479 0006 0019 4369 :50 by gereddy....Ci
220 : 7363 6F20 5753 2D43 3335 3530 2D32 342D 5057 5200 sco WS-C3550-24-PWR.
240 : 0200 0800 0000 0000 0300 1346 6173 7445 7468 6572 ...........FastEther
260 : 6E65 7430 2F31 0004 0008 0000 0028 0008 0024 0000 net0/1.......(...$..
280 : 0C01 1200 0000 00FF FFFF FF01 0221 FF00 0000 0000 .............!......
300 : 0000 1380 81C8 00FF 0000 0009 0006 4564 000A 0006 ..............Ed....
320 : 0064 000B 0005 0100 1200 0500 0013 0005 0000 1600 .d..................
340 : 1100 0000 0101 01CC 0004 0000 0000 001A 0010 0000 ....................
360 : 0001 0000 0000 FFFF FFFF ..........
DTP
R1(PKTS:2 of 3)#sh 3
=============================================================================
00:27:18.415 UTC Fri Mar 1 2002 Relative Time: 24.271971
Packet 3 of 3 In: FastEthernet0/0
Ethernet Packet: 60 bytes
Dest Addr: 0100.0CCC.CCCC, Source Addr: 0013.8081.C801
IEEE 802.3 length: 36
LLC DSAP: 0xAA, SSAP: 0xAA, Control: 0x03
SNAP OUI: 0x00000C, Protocol: 0x2004
Data:
0 : 0100 0100 0745 6400 0002 0005 8100 0300 05A5 0004 .....Ed.............
20 : 000A 0013 8081 C801 0000 0000 0000 0000 0000 ..................
Conclusion
DTP frames have no association with a vlan and hence are never tagged.
IEEE BPDUs have no association with a vlan and hence are never tagged.
CDP & VTP both belong to vlan 1, if native vlan is 1 they will be untagged, if the native vlan is anything other than 1 they will all be tagged with 1.