Keystore type: which one to use?
By looking at the file java.security of my JRE, I see that the keystore type to use by default is set to JKS. Here, there is a list of the keystore types that can be used.
Is there a recommended keystore type? What are the pros/cons of the different keystore types?
Answer
There are a few more types than what's listed in the standard name list you've linked to. You can find more in the cryptographic providers documentation. The most common are certainly JKS (the default) and PKCS12 (for PKCS#12 files, often with extension .p12 or sometimes .pfx).
JKS is the most common if you stay within the Java world. PKCS#12 isn't Java-specific, it's particularly convenient to use certificates (with private keys) backed up from a browser or coming from OpenSSL-based tools (keytool wasn't able to convert a keystore and import its private keys before Java 6, so you had to use other tools).
If you already have a PKCS#12 file, it's often easier to use the PKCS12 type directly. It's possible to convert formats, but it's rarely necessary if you can choose the keystore type directly.
In Java 7, PKCS12 was mainly useful as a keystore but less for a truststore (see the difference between a keystore and a truststore), because you couldn't store certificate entries without a private key. In contrast, JKS doesn't require each entry to be a private key entry, so you can have entries that contain only certificates, which is useful for trust stores, where you store the list of certificates you trust (but you don't have the private key for them).
This has changed in Java 8, so you can now have certificate-only entries in PKCS12 stores too. (More details about these changes and further plans can be found in JEP 229: Create PKCS12 Keystores by Default.)
There are a few other keystore types, perhaps less frequently used (depending on the context), those include:
PKCS11, for PKCS#11 libraries, typically for accessing hardware cryptographic tokens, but the Sun provider implementation also supports NSS stores (from Mozilla) through this.BKS, using the BouncyCastle provider (commonly used for Android).Windows-MY/Windows-ROOT, if you want to access the Windows certificate store directly.KeychainStore, if you want to use the OSX keychain directly.