The copying should work without a problem, but if you happen to upgrade to Snow Leopard at the same time, you might run into some compatibility issues, depending on the "ports" you have installed. Same goes for old "ports" that may have been specifically built for your old system (maybe processor dependent), you could run into problems there, too.
Remember to run selfupdate, and upgrade the installed ports (where needed).
Apple has a very nice explanation of how Migration Assistant works, what steps and accessories you need and much more:
In a nutshell, Migration Assistant has three bins of data to move:
- Applications (just the programs - no user data or settings transfer)
- Users (the user data, settings, preferences, saved files and such - but no Applications. You could have all your Word docs, but no Word to edit them in this case)
- Everything else that's not an App or a User. This gets oddball things like /Users/Shared files and folders that don't belong to one user, unix and command line tools like homebrew that get installed outside /Applications and /Users.
So with three check marks (let's assume you don't have multiple users), there are 7 combinations you could migrate - each leaving a different set of data on the destination Mac. (If Applications was A, Users was B, and Everything else C) You could combine them as follows: A, B, C, A+B, B+C, A+C, or A+B+C
I would say, you get to experiment when you get your new Mac. Run the migration you think is best, and then test it. If you don't like it, erase the destination Mac (booting into recovery mode, erasing the HD and re-install a clean OS might take 25 minutes on a fast network - the OS download is 4 Gb or so) and re-run the assistant.
For me, I would recommend both migrating from your Backup and then optionally re-migrating from the old Mac. It's important to test your backup - when was the last time you tested a restore to be sure you have a viable backup?
Everyone says "make sure you back up" but they really mean and might be better saying is, "make sure you can restore your backup and it has what you need!"
I would encourage you to configure your Time Machine on the old Mac to exclude any things you don't want moved to the new Mac, make a back up and write down the time of the back up. Then eject the backup drive and change the backup settings to back everything up again.
You could take that "latest" backup and Migrate it to the new Mac and test for a while (re-connecting the backup drive to the old Mac) to keep your "main" Mac backing up.
As you test the new mac for a day or so, you can decide it's time to move over. At that point, turn off Time Machine on the old Mac and connect the backup drive to the new Mac. It will offer to "inherit" the old backups and you can move forward. Worst case, you still have the backups to restore something needed and then can clear the old Mac for donation, sale or mothballing.
Best Answer
While generally speaking, you can simply copy an app bundle from one Mac to another, it doesn't carry over the user data and app preferences that the app generates and stored elsewhere (generally somewhere in users home directory).
Also, not every app Mac installs as a .app bundle and may have installed files elsewhere, causing the copying over .app bundle approach to not work well.
Recommended approaches that you can take are:
Reinstall the apps from source. It could be either Mac App Store, Homebrew Cask or direct download from the publishers website. This way you'd get the apps installed afresh and in the way the developer intended.
Also, even if some of the apps are paid, most Mac apps come with a licenses that lets you use them on all of your personal Macs.
This approach may have a drawback where you may lose app specific preferences and data (not necessarily user data but data such as plug-ins which is directly managed by the app).
However, this approach would be the most likely recommended one as it would let you have a clean install.
If you are concerned about losing app specific configuration and app data, you may consider using Migration Assistance or restoring to the new Mac via a Time Machine backup.
The benefit here would be that you can technically set your new Mac to be in the same state as the old one.
Once you have your new Mac setup, you can then normally uninstall the apps that you don't need, and, get rid of any data that got carried over and is not needed on the new machine.
So to conclude, if the app that you are looking to transfer was installed simply as a .app bundle, has not installed anything outside, and doesn't have any customisations that you care about losing, you'd be safe copying it over. (But then again, what's possibly preventing you from re-installing them from source?)