Seconded. Group 14 (2048-bit, ≈112-bit workfactor) or another safe 2048-bit or greater prime (such as ffdhe2048, or ffdhe3072 @ ≈128-bit workfactor) will do fine for now. You don't need to roll your own safe primes. As per the paper: "When primes are of sufficient strength, there seems to be no disadvantage to reusing them."
The problem with reusing them is of course when they're not strong enough, and so if an adversary can pop one, they can get a lot of traffic - and as I've said for a while and as the paper makes clear, 1024-bit and below are definitely not strong enough. Anything below 2048-bit would be a bit suspect at this point (which is precisely why the TLS Working Group rejected including any primes in the ffdhe draft smaller than that - even though a couple of people were arguing for them!).
If you're still needing to use 1024-bit DH, DSA or RSA for anything at all, and you can't use larger or switch to ECC for any reason, I feel you have a Big Problem looming you need to get to fixing. Custom DH groups will not buy you long enough time to ignore it - get a plan in place to replace it now. We thought 1024-bit was erring on the small side in the 1990s!
I concur that the NSA's attack on VPN looks like an operational finite-field DH break - I didn't realise that two-thirds of IKE out there would still negotiate Oakley 1 (768) and 2 (1024), but I suppose I didn't account for IKE hardware! Ouch!
Their attacks on TLS are, though also passive, architected far more simply and more suggestive of an RC4 break to me as there seems to be no backend HPC needed - ciphertext goes in, plaintext comes out. Both are realistic attacks, I feel, but RC4 would have been far more common in TLS at the time than 1024-bit DHE, and although 1024-bit RSA would be present many likely sites would have been using 2048-bit, so naturally they'd go for the easiest attack available. (That gives us a loose upper bound for how hard it is to break RC4: easier than this!) I also don't think the CRYPTO group at GCHQ would have described this as a "surprising […] cryptologic advance" from NSA, but just an (entirely-predictable) computational advance, and (again) lots of people in practice relying on crypto that really should have been phased out at least a decade ago. So there's probably more to come on that front.
Best current practice: Forget DHE, use ECDHE with secp256r1 instead (≈128-bit workfactor, much faster, no index calculus). You can probably do that today with just about everything (except perhaps Java). It will be faster, and safer. And, we know of nothing wrong with NIST P-256 at this point, despite its murky origins.
Looking forward, Curve25519 (≈128-bit) and Ed448-Goldilocks (≈222-bit) are, of course, even better still as the algorithms are more foolproof and they are "rigid" with no doubts about where they come from (and in Curve25519's case, it's even faster still). CFRG is working on recommending those for TLS and wider standardisation. You can use 25519 in the latest versions of OpenSSH right now, and you should if you can.