The plus side is that GnuPG by design has a relatively limited attack surface. It's tough to conduct a side-channel attack that requires thousands of message stimulus-response tests to get a single key or message bit, given that each iteration of that attack will (in typical GPG usage) require manual intervention.
As long as your crypto isn't "online", GPG is still a pretty safe bet. You can't say the same thing about a lot of newer crypto libraries.
However, if you're doing something like encrypting a session cookie, you should use Nacl, not GPG.
It's very tempting, especially for smart, multilingual, incredibly talented individuals to just roll this as if the libraries below you don't matter. Crypto is, unfortunately, the leakiest of the leaky abstractions you can end up building on. No matter what, I always have someone else (and preferably several someone elses) check my work when it comes to authentication systems and encryption.
IANAL,EIIWTWNBFLA,UHTPMTGMROOTS. tpateck is a much better person to talk to than me if you need to find someone to help you deal with these issues most subtle.
How long do you think that will last when everyone encrypts all their email?
That's how I understood it anyway!
Here's what they've found lately:
CVE-2014-4617 (DOS only)
CVE-2013-4576 (RSA Key Extraction via Low-Bandwidth Acoustic Cryptanalysis -- awesome, but not exactly practical)
CVE-2013-4402 (DOS only)
CVE-2013-4242 (RSA side channel attack)
CVE-2012-6085 (invalid keys could corrupt memory)
-- 5 years with not a single security hole --
CVE-2007-1263 (bug in signed message verification)
Compare this with the security history of the browser you are using to view this comment, and weep..