After downloading a .crx file, Google Chrome installs the extension into a randomly generated directory in ~/Library/Application Support/Google/Chrome/Default/Extensions and registers it in its Preferences file.

To remove an extension

1. Close Google Chrome
2. Open ~/Library/Application Support/Google/Chrome/Default/Preferences in a text editor
3. Search for the extension and write down its id
4. Remove it from the settings element
5. Go to ~/Library/Application Support/Google/Chrome/Default/Extensions
6. Remove the directory with as name the id from above
7. Start Google Chrome

For example

Lets remove an extension that provides a toolbar icon for Google Reader. In the Preferences file this is registered using the id cciomicmolmofdcijoabgmccejjbacgg

....
"extensions": {
  "autoupdate": {
     "last_check": "12900842060608418",
     "next_check": "12900863894021384"
  },
  "settings": {
     "cciomicmolmofdcijoabgmccejjbacgg": {
        "location": 1,
        "manifest": {
           "background_page": "tpgr.html",
           "content_scripts": [ {
              "js": [ "feedLine.js", "makeRequest.js", "tpgr_cs.js" ],
              "matches": [ "http://*/*", "https://*/*" ]
           } ],
           "description": "Google Reader on the toolbar. Extension by TPReal (tpreal@gmail.com)",
           ....
     },
     "kebibidoobkefhegbnfmlkcejmaebblf": { 
     ....
     },
 ....

After removing the setting for cciomicmolmofdcijoabgmccejjbacgg the Preferences file looks like this:

....
"extensions": {
  "autoupdate": {
     "last_check": "12900842060608418",
     "next_check": "12900863894021384"
  },
  "settings": {
     "kebibidoobkefhegbnfmlkcejmaebblf": { 
     ....
     },
 ....

Now simply remove the directory using rm -rf '~/Library/Application Support/Google/Chrome/Default/Extensions/cciomicmolmofdcijoabgmccejjbacgg' in the Terminal.

Edit

Hehe, going to chrome://extensions/ is a lot easier, didn’t know that