Landesk is ok (I haven't used it more then about 2 hours during a trial run)
I have used (and it's ok too) Altiris tools, and there are a dozen other ones that can do "Software Metering" i.e. how long is each app open/being used. Some apps are smarter then others, and will look at the focused window as well as open (so it doesn't say "they were browsing the web all day" just because IE was open, but minimized).
Software metering does require an agent. There are some inexpensive, smaller software metering apps out there, can't remember names. You should look at Asset/software/license management, as that's where you will find metering stuff. If you are an MS partner, they have one that does some of this (SMS??), but it was a bit cludgy compared to the 3rd party stuff (imho)