At this point I think it's best to assume that seized sites were brought down through some combination of the following:
OpSec mistakes - sites registered under personal e-mail addresses, administration from the United States, large personal exchanges of bitcoin for fiat, etc.
Site vulnerabilities - exploits, hosting co-location with other hidden services, etc.
Tor exploit/traffic analysis - More on this here
Bullets (1) and (2) mostly involve idiosyncratic risks that need to be managed by individuals and sites, and I expect Onymous will stimulate greater vigilance.
Bullet (3) though is something that affects everyone and is in many ways a public good, so there's less obvious individual incentive to improve/fix it. But given the international coordination that Onymous was supposedly executed with (including the FBI and Europol), I think it's best if we assume they are all running their own Tor nodes with the intention of trying to analyze the traffic to narrow down possibilities of where sites and individuals are located.
Any decentralized system can be disrupted if a sufficient number of nodes are maleovelent. Outside of technical sophistication of the protocol and its implementation in software, increasing the number of known honest nodes can help prevent this type of attack.
There have been questions about whether sites should migrate to an alternative to Tor (e.g., I2P or Freenet). Given the network effects that Tor currently benefits from and as I see it fairly similar problems with those alternative protocols, we should probably continue to invest in Tor for the time being.
So to keep this solution oriented, here are some great ways to support the Tor network:
Run your own Tor node Note: exit nodes are the most important, since they are the most persecuted and are very useful for traffic analysis
Donate to the Tor project Accept Bitcoin
Donate to Noisebridge to fund exit nodes Accept Bitcoin
Donate to torservers.net to fund exit nodes Accept Bitcoin
In addition to supporting the above, you should also consider donating to fund TAILS development (they accept bitcoin as well)
TL;DR it's imperative that the DNM communities invest in more honest Tor nodes and funding to the Tor Project. Every honest node we have reduces the power of traffic analysis from a coordinated adversary.
Final words
The task of hiding the location of low-latency web services is a very hard problem and we still don't know how to do it correctly. It seems that there are various issues that none of the current anonymous publishing designs have really solved.
In a way, it's even surprising that hidden services have survived so far. The attention they have received is minimal compared to their social value and compared to the size and determination of their adversaries.
It would be great if there were more people reviewing our designs and code. For example, we would really appreciate feedback on the upcoming hidden service revamp or help with the research on guard discovery attacks (see links above).
Also, it's important to note that Tor currently doesn't have funding for improving the security of hidden services. If you are interested in funding hidden services research and development, please get in touch with us. We hope to find time to organize a crowdfunding campaign to acquire independent and focused hidden service funding.