So I have been trying to get meterpreter as undetected as possible by most major AV softwares and I think I have come close to succeeding. I downloaded the AVG internet security installer, and using SET (wont let you do it with ./msfencode says extra junk at end) choose option 4 to make your own back door, choose 2 (windows/meterpreter/reverse_tcp) and then choose options 16 to make your own back doored executable, please note that you will have to set the path to your legit exe in the set_config.
Code:
#CUSTOM EXE YOU WANT TO USE FOR METASPLOIT ENCODING, THIS USUALLY HAS BETTER AV
# DETECTION. CURRENTLY IT IS SET TO LEGIT.BINARY WHICH IS JUST CALC.EXE. AN EXAMPLE
# YOU COULD USE WOULD BE PUTTY.EXE SO THIS FIELD WOULD BE /pathtoexe/putty.exe
CUSTOM_EXE=/root/AVGInstaller.exe
Change the red to the path of your exe. Here is the results from Virus Total

If you can it more undetectable then please post here!

Antivirus results
AhnLab-V3 - 2010.10.10.00 - 2010.10.09 - -
AntiVir - 7.10.12.167 - 2010.10.08 - -
Antiy-AVL - 2.0.3.7 - 2010.10.10 - -
Authentium - 5.2.0.5 - 2010.10.10 - -
Avast - 4.8.1351.0 - 2010.10.10 - -
Avast5 - 5.0.594.0 - 2010.10.10 - -
AVG - 9.0.0.851 - 2010.10.10 - -
BitDefender - 7.2 - 2010.10.10 - Backdoor.Shell.AC
CAT-QuickHeal - 11.00 - 2010.10.09 - -
ClamAV - 0.96.2.0-git - 2010.10.10 - -
DrWeb - 5.0.2.03300 - 2010.10.10 - -
Emsisoft - 5.0.0.50 - 2010.10.10 - -
eSafe - 7.0.17.0 - 2010.10.07 - -
eTrust-Vet - 36.1.7901 - 2010.10.08 - -
F-Prot - 4.6.2.117 - 2010.10.10 - -
F-Secure - 9.0.15370.0 - 2010.10.10 - Backdoor.Shell.AC
Fortinet - 4.2.249.0 - 2010.10.10 - -
GData - 21 - 2010.10.10 - Backdoor.Shell.AC
Ikarus - T3.1.1.90.0 - 2010.10.10 - -
Jiangmin - 13.0.900 - 2010.10.10 - -
K7AntiVirus - 9.65.2713 - 2010.10.09 - -
Kaspersky - 7.0.0.125 - 2010.10.10 - -
McAfee - 5.400.0.1158 - 2010.10.10 - -
McAfee-GW-Edition - 2010.1C - 2010.10.10 - -
Microsoft - 1.6201 - 2010.10.10 - Trojan:Win32/Swrort.A
NOD32 - 5518 - 2010.10.09 - a variant of Win32/Rozena.AH
Norman - 6.06.07 - 2010.10.10 - -
nProtect - 2010-10-10.01 - 2010.10.10 - Backdoor.Shell.AC
Panda - 10.0.2.7 - 2010.10.10 - -
PCTools - 7.0.3.5 - 2010.10.10 - -
Prevx - 3.0 - 2010.10.10 - -
Rising - 22.68.05.00 - 2010.10.09 - -
Sophos - 4.58.0 - 2010.10.10 - -
Sunbelt - 7031 - 2010.10.10 - -
SUPERAntiSpyware - 4.40.0.1006 - 2010.10.10 - -
Symantec - 20101.2.0.161 - 2010.10.10 - -
TheHacker - 6.7.0.1.054 - 2010.10.10 - -
TrendMicro - 9.120.0.1004 - 2010.10.10 - -
TrendMicro-HouseCall - 9.120.0.1004 - 2010.10.10 - -
VBA32 - 3.12.14.1 - 2010.10.08 - -
ViRobot - 2010.9.25.4060 - 2010.10.10 - -
VirusBuster - 12.67.11.0 - 2010.10.10 - -
File info:
MD5: afc2d27e8b78b2db772a2e9fa9de42d6
SHA1: 521a2200abbef8e171a4b7eecd50b1685c22dcde
SHA256: 3830cee855ab4cbab0db125e73afcbeb6ec713fec1eea82a35 c08bee0e8d8086
File size: 4283672 bytes
Scan date: 2010-10-10 20:30:16 (UTC)