They both have features the other lacks: the order form is better with HostBill, the but the client area is better laid out with WHMCS. I personally find the admin area of WHMCS easier to use, and it integrates better with accounting software (Kashflow, Xero) than HostBill.
Last time I checked there were a lot of spelling and grammatical errors on HostBill's site which really turned me off from looking into it further. Hopefully they've cleared that up but I guess it's true that you only get one first impression.
HostBill looks much better and their development is on going to add features. WHMCS has been in the business longer, pretty much stable not so much on the looks but they can be customized with either of the scripts.
We personally use WHMCS, but I have also got a free 1 year key for doing something of HostbillAPP, and the only good thing I can say about hostbill is the order/check out method is pretty sweet over WHMCS, but I wouldn't be surprised if WHMCS does a update soon to make something better.
I would always pick WHMCS over HostBillAPP just for the simple reason that it's more known, and I know it's secure, and it will be around for awhile hostbill is fairly new and I personally didn't like the setup/management of it for the admin area or client area. The only thing I did like was the java script order checkout, slider packages and so on.
WHMCS is more easier to use, better management, and a great service to have for your company. I would never change from WHMCS or suggest the transition to HostBill from WHMCS.
WHMCS does everything we need, and it's easy to customize and do what we need. We have done our own setups, and in-house modules for our services, and trying to do anything with hostbill is much more harder then it is with WHMCS, WHMCS has a clean interface and very easy to use, manage, and navigate through hostbill feels cluttered to me.
+1 for WHMCS.
I also think the way they offer there pricing should be flipped between WHMCS and HostBill (how hostbill don't offer monthly keys) just for the fact that hostbill is new, even though they offer a trial it's a small trial and it don't give users the full advantage of fully using it to decide if they wanna purchase a year/owned key.
WHMCS on the other hand has been around and proved it's service to be one of the best and I could see them removing there monthly key package but to be honest i doubt they will because it's where they're making money at also for new company's and stuff to take off don't have the money i guess to blow on a yearly licenses if they are not doing very big services and such (a small shared hosting provider), and I think HostBill will lose alot of potential customers as that's what pushed me away from even purchasing it to try it, or even trying the trial as they didn't even offer a monthly service of it; which in my eyes is a bad business practice for a company/application that's fairly new to the market/game.
The only reason I did give it a try was because as I stated above I obtained the HostBill owned licenses for free.