There is the gnome-keyring-daemon and seahorse which makes key & password management very easy.
Basically if you're running gnome-keyring-daemon as a gpg agent, it has the ability to unlock your GPG keys automatically. It does this by maintaining a password keyring, which contains the passwords to things like web sites, GPG keys, SSH keys, etc. This password keyring is then secured with it's own password. So you unlock it, and the gnome keyring unlocks everything else.
As an added bonus, gnome-keyring-daemon has a "login" keyring, which if it's password matches your user password, the keyring is automatically unlocked when you log in.
Configuration
How to get this working? Just install gnome-keyring-daemon and seahorse. The package should do all the system configuration for you. Just make sure you're not starting another keyring daemon or GPG agent. Whichever starts last "wins", and the gnome keyring starts in the PAM stack, so extremely early.
If your GPG keys are stored in ~/.gnupg, it will automatically pick them up and act as the GPG agent for them. Same goes for SSH keys stored in ~/.ssh
The first time you try to use the private key, you'll get a dialog that looks like this: (I triggered it by a simple command line gpg -d myfile.gpg) 
Just select "Automatically unlock this keyring whenever I'm logged in"
Now we haven't really talked about seahorse. That's because it's not strictly necessary. All this has been done with just the regular gnome-keyring-daemon. However with seahorse you can view and manage all your keys & keyrings. And if you use centralized authentication (LDAP), you'll need to use it when you change your login password to also change the password on the "login" keyring to match it.
Other passwords
As alluded to earlier, gnome-keyring-daemon can also store web site passwords. Last time I checked chrome supports this, but firefox does not. However there is one trick to getting it working.
By default you'll have 2 keyrings, a "login" keyring, and a "default" keyring. The "default" keyring is the default (hence the name). But it's a separate keyring, so it doesn't automatically get unlocked. In seahorse, if you right-click the "login" keyring, there's an option to "set as default". Select this and it'll start getting used for passwords. I personally just delete the "default" one and use "login" for everything.
The GPG man page has several options you're probably interested in, that you could work into your own personal decrypt-edit-encrypt script/function. Like:
--passphrase-fd n - Read the passphrase from file descriptor n--passphrase-file file - Read the passphrase from file file... Obviously, a passphrase stored in a file
is of questionable security if other users can read this file.
Don't use this option if you can avoid it.--passphrase string - Use string as the passphrase... Obviously, this is of very questionable
security on a multi-user system. Don't use this option if you
can avoid it.
Placing a keyfile in ram (tmpfs) and not readable by anyone else might be adequate. Or for Linux you could look into the kernel's key management facility i.e. keyctl
Best Answer
I solved the problem by upgrading gnupg from 1.4 to 2.1 which seemed to simplify a lot the configuration.
However, it generated an error of migration of the secret key between gpg and gpg2.
gpg2 generated the following error message when I was requiring password from pass:
The solution came from this previous issue:
with [ID] being the id of my key. It imports correctly the keys from gpg to gpg2.
Finally I rebooted and now my passphrase is cached, which makes me a really happy user of pass.