There are a few out there, depending on what kind of a car you want. Here is a url for a fairly comprehensive list. http://www.cartalk.com/blogs/bestride/these-are-all-manual-transmission-cars-available-today
Some are only available on stripped cars, a few are available with options. I know Subaru offers the Impreza, Crosstrek, and Forester with a manual and lots of options, all are AWD and I believe still towable 4 down with a manual. Mazda likes to market themselves as a enthusiast brand and offers manuals in the 3,6,and CX5. Honda also offers a manual in many vehicles and configurations, including the Accord coupe with 278hp V6 and any trim except Grand Touring. The fit is a popular toad and can be hadi in LX or EX trims with a stick. European brands offer a few more options as well.
OP, as a die hard manual transmission guy I feel your pain. I refuse to buy something for myself to drive without a stick. The Expedition is the wife's / family / tow vehicle. My commuter is a focus ZX3 5spd
