Not exactly mainstream apps, but could always be useful to somebody else...
Atmel AVR Studio 4.12 and SP3 for Atmel AVR Studio 4.12:
Both use an Installshield installer (-R to record to setup.iss, -s for silent install). Select W/O USB driver if you don't want that to popup (can easily be installed later, and no use unless you've got like a USB JTAG ICE or such)
Software for Tekpower lab equipment (multimeter, adj power supplies, etc - for RS232 comms) uses installshield as well (same switches, -R, -s)
CodeVisionAVR C Compiler: password protected Inno installer:
setup.exe /VERYSILENT /SP- /PASSWORD=passwordgoeshere
ImageCraft ICCAVR seemingly has no switches (home made installer?) You have to capture/repack it.
I'll spare you guys the really weird/unusual stuff

[edit] More stuff:
PerfectDisk Command Center 8
Installshield
-r to record, -s [-f1] [-f2] as usual
WinMerge 2.4.10
Inno
/VERYSILENT /SP-
SQL2005 Service Manager 1.0.0.10
MSI
/qb or /qn
Unleash It v2.4.1.0
NSIS
/S
GhostDoc 1.9.5 (for 2005; v1.3.0 for 2003)
MSI
/qb or /qn
The Regulator 2.03
MSI
/qb or /qn
Console 2.00 Beta
No installer!
Use $OEM$ or make a SFX