I have a MacMini running OS X 10.6.4 with ImageCapture and it remembers my last folder location, scan settings and the last file name.
I worked on a new MacBook Pro running OS X 10.6.4 and went to configure Image Capture and it wouldn't remember any setting changes: not the "other" folder I scanned to, nor the name, nor the PDF or color option. I searched the web for instructions on setting ImageCapture preferences and found lots of fairly technical suggestions because ImageCapture doesn't have a Preferences option any more.
I gave up, but not before scanning several times (didn't count but at least 6 times), and each time re-specified a scan-destination folder, which I'd created in the Documents folder, plus changed other scan settings).
Then I started ImageCapture one more time and low and behold, it had all the settings from my last scan! Hurray! Plus, if I changed the scan type from PDF to jpeg and quit Image Capture, it retained the new info.
That Steve Jobs.... Often forcing new ways of doing things on users.
So on 2 Macs running 10.6.4, they both now retain their custom ImageCapture preferences merely by using Image Capture (it detected my preferences).
It seems kind of "out there," and maybe there's something else going on, like a bug where ImageCapture doesn't retain user settings until the 6th or 7th or some nth Quit.
Anyway, if the apparent lack of Image Capture preference control ticks you off, try this: change ImageCapture's settings, scan something, quit, then repeat several times. After 5-10 times you should notice your preferences "sticking" if what happened for me on two Macs wasn't a fluke.