Desktop! I use both for work.
Desktop has its advantages:
1) Can open multiple windows at a time. Cannot do with online version.
2) You can adjust the bank reconciliations if something goes wrong somewhere along the way. Cannot undo and re-do bank reconciliations in the online version, so you almost need to do them perfectly, or remember any prior adjustments and journal entries that you do when the balance changes. (Not a great internal control feature, but at least you can lock/close the books with a password in the desktop edition to prevent changes after a certain date)
3) Cost – can use the old desktop versions forever, just don't “update” as the prompt suggests. (I'm using a 2007 edition!) If you stop your subscription to online, at some point your data will be held at ransom, i.e. you will be given a warning to pay up or lose access to your data. Am experiencing that now, but at least the data is old enough that it's become somewhat insignificant.
4) Classes – can be turned on/off, if you like to track things in a certain way, so that your list of accounts and classes aren't crazy long if you use them in a chronological fashion.
5) Not attached to web and QB technical issues – I've been locked out when QB online goes down.
Online is not completely bad:
1) Searches and reports – I admit are a little bit more interesting and robust with the online edition.
2) Easily accessible anywhere with a web browser. The same can be said if the desktop edition is set up as a server.
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