Recently we wanted to book a weekend away in a NSW country town, staying at a motel, farmstay or something similar. We headed to Wotif to find what was available for our dates in the town we wanted. We read through the list and investigated a couple, and eventually decided on a farmstay. We were in the process of booking, but found that there was a $4.95 booking fee for using the Wotif site, which personally I'd rather not pay. (Call me cheap, but I like to save where I can!)
I suggested that we check the farmstay's own website to see if there was any difference in the rates. There was! In the end, by phoning and making the booking directly with the farmstay, we saved just under $40 for one night's accommodation. Yes, it cost us a phonecall, but we would have had to be on the phone for an awful long time for us to cancel out that $40 saving!
Also, instead of having to pay the full amount up front, we only had to pay a half-rate deposit upfront.
We did find the "last minute" website useful for browsing a good list of available properties, quickly and easily getting an overview of the ones that interested us, and seeing which were available on the dates we required.
However, it certainly pays to check the establishment's own website if they have one, or even just call them to see if they have cheaper rates than the "last minute accommodation" type websites.