As cheap alternative to the bookstand + external keyboard combination already mentioned, I find it very useful to simply wedge a small flat object (I use a marker) under the back of the laptop while it's resting on a desk. This puts the keyboard at a slight angle, which I found much more comfortable for prolonged typing (keeps the wrist from pressing on the edge too hard).
It also provides some extra ventilation (that's why I originally did it), as the wrist rests can get uncomfortably hot sometimes on my MBP.
You can also use an external monitor with your external keyboard in front of it and leave the laptop somewhere to the side to use as 2nd screen.
The first thing to do is go to System Preferences » Security & Privacy and enter your name and phone number in the "Show a message when the screen is locked" field. That will give someone who finds your computer a chance to return it to you.
To address the specific issue that you raised about Applications:
You can install the Applications to ~/Applications (that is, create an "Applications" folder inside your home folder) and install apps there instead.
Note that the Mac App Store will automatically install apps to /Applications but you can easily relocate them. You could even automate the process using Hazel or something like it.
Other ideas:
launchd is your friend. You can create scripts or programs which will run whenever anyone is logged into your computer, or you can do the same for when specific users log in. For example, create a new Gmail account and create a script which will send the IP address of your computer every 15 minutes:
curl -s http://whatismyip.org | Mail -s "$HOST address as ofdate" yournewaddress@gmail.com
(Note: you will have to setup your Mac to send email from the command line. I wrote a HOWTO for that.)
DynDNS is another good idea. That will give you a hostname to use with ssh. (Be sure that "Remote Login" is enabled via System Preferences » Sharing.) Make sure that it works (i.e. daemon runs/updates) while you are logged into your 'dummy' account.
My Preference
I set a Firmware Password on my Mac so they can't boot from another drive (i.e. trying to wipe it) without entering a password.
I use FileVault 2 (Lion) to encrypt my drive. They only get access to Safari. See Can FileVault 2 and Find My Mac foil thieves? for more details (I didn't write that, I just recommend it).
In sum: I do as much as I can to protect my data, and I do as much as I can to give someone the opportunity to return it if I lose it and they find it (vs being stolen).
I have thought about (but have not actually checked to see if it can be done) going to a jeweler and asking to see if they can inscribe my name / phone number on the bottom of my MacBook Air.
Those are my thoughts, FWIW.
Best Answer
Here is a possible solution for you.
Normally you would not need additional (forced) ventilation since MacBook does that as long it gets fresh air access.