As said in the comments above, you won't be able to change that on a large scale basis. Applications calling Terminal.app will do that by calling its Bundle identifier,
com.apple.terminal. You'd have to change this to "fake" the Terminal and redirect to another one. Is that's possible? I highly doubt so.
This means that every application calling Terminal will have a setting for the bundle identifier used. Some will probably have that hardcoded, others should allow changing it, either through Preferences or through a preference list setting.
How to make BBEdit use another Terminal
For BBEdit, that's relatively easy according to the release notes. This is for version 8.7 though, and I can't find it in the "Experts Preferences" of version 10 anymore. Maybe they've removed the feature.
defaults write com.barebones.bbedit Misc:TerminalBundleIDOverride "com.googlecode.iTerm2"
com.apple.Terminal with the bundle identified of the other terminal emulator, e.g.
com.googlecode.iterm2 for iTerm2.
A similar entry can be found on secrets.blacktree.com, although it doesn't appear to be working (I've never seen a
-bundleid datatype in
The best idea would be to bring up a support request with BBEdit's developers.
How to make Alfred use another Terminal
Alfred's shell extensions use the terminal emulator you specify, according to the help.
You can select to use the OS X Terminal.app or iTerm, as well as your prefix for Shell commands in the Alfred preferences.
It didn't work for me at first, so I had to delete iTerm.app, delete Alfred and its preferences/caches, then reinstall iTerm2. This is explained in the Alfred support forums.