Probably the biggest annoyance to using multiple monitors is that Remote Desktop will only pass through information on the default monitor. So if you have two (or more) monitors at work, and two at home, you can't get the benefit of the extra monitors if you're connected remotely. Sometimes, if there's a window that you want on your second monitor at work, you can right-click the taskbar icon and use Move; but sometimes that doesn't work, and the window isn't available at all. It's usually safest to move every window to your default monitor before leaving for the day, but that's easy to forget.

LogMeIn -- https://secure.logmein.com/go.asp?page=home -- is a free browser-based utility that lets you see the full extent of your desktop remotely. You can open a browser at home, stretch it across your extended desktop, connect to your office computer, and see the contents of all your monitors. Unfortunately, it's too slow for general use, maybe because the company is in Massachusetts and the round-trips kill performance. It can save some aggravation if you want to get at a window on your second monitor and can't, though -- you can use LogMeIn to move it onto your default monitor, and then get at it through Remote Desktop.

I've read that pcAnywhere from Symantec handles remote multiple monitors, but it's also $199.99. Maybe the Windows Vista version of Remote Desktop will have multi-monitor passthrough next year.

This site has all kinds of multi-monitor info: http://www.realtimesoft.com/multimon/