I hate programs that always put junk in C:\Progra~1. I've put my programs in C:\ since my pre-Win95 DOS and OS/2 days. IMHO there's nothing wrong with installing in the root of the drive, especially if it's only a default that you can change if you want to.
In fact, as far as I'm concerned, InstallShield(R) Wizard -- and the idea of installers in general -- is a piece of crap. I want my installer to be an editable batch file that just copies the files to C:\ -- and does any other setup if necessary. Not that other setup is usually actually necessary, but a lot of apps feel a need to call home over the Internet, install a ton of stuff on my desktop, my Start menu, my Windows directory, all over the Registry, etc., as well as transfer the damn executable from the CD-ROM to my hard disk, which is all a well-written program should really need to do.
I want to actually see what the program's doing, so I can keep track of the pieces. I can't count the number of times I've had to delve into C:\Users\Whoever\Applic~1 or C:\Progra~1 or C:\Progra~2 (on 64-bit Windows) or C:\IDontEvenKnowWhat\Users\Whoever\Whatever\Profiles\Roaming\TheCompany\TheApp to find my saved game so I can continue my adventure on another PC. Or had to regedit.exe into HKEY_LOCAL_MACHINE\Software\TheCompany\TheApp\TheSetting and edit some hex value when a plain-text configuration file in C:\PROGRAM would have been perfectly adequate.
I've been using Linux for years now, and frankly it isn't much better -- install $PKG and you might get /usr/bin/$PKG, /usr/lib/$PKG, /usr/share/doc/$PKG, /usr/share/$PKG, /var/$PKG, /var/log/$PKG, /var/run/$PKG, /etc/$PKG, /etc/init.d/$PKG, /var/www/$PKG, /home/$USER/.$PKG -- part of the reason for having a package manager is to stay in control of this sprawl. The simple and obvious solution of putting $PKG in /$PKG or /opt/$PKG is too much to ask, of course, since it breaks compatibility with the first UNIX where /usr/bin is different from /bin because the system outgrew the specific hard drive the developers were using, so they had to split some things off into a second drive, which was mounted at /usr.