June 2019: This FAQ is currently being rebooted -- most of the existing entries were outdated and rarely raised in user forums seven years after Whonix's founding. All the previous contents were moved to more appropriate places in the existing documentation. It is possible to find those entries with the Whonix wiki internal search or via an internet search engine. The old version of the FAQ can still be found here. As contemporary, frequently asked questions are identified, they will be added here.
Why aren't the SKS Keyserver Wiki Steps always Functional?
The SKS keyserver network has recently come under attack after a critical vulnerability was discovered which allows certificates to be spammed using a flaw in the OpenPGP protocol itself. Future releases of OpenPGP software will likely mitigate this flaw, but high profile contributors to the protocol suggest that data should not be retrieved form the network at present if possible. For more details, see here.  
Virtual Private Networks
Should I Set Up a VPN with Whonix?
In a word, no. There are several reasons for this position: 
- It is impossible to verify a VPN provider is actually trustworthy and not logging data -- 'honeypot' providers might be ubiquitous.
- VPN traffic is sensitive to Deep Packet Inspection (DPI) and Website Traffic Fingerprinting,  so it is ineffective in hiding use of Whonix ™ and Tor from the ISP or skilled adversaries.
- Depending on the configuration, VPN tunnels combined with Tor can worsen anonymity. For example it can lead to a permanent Tor exit relay in the network or remove Stream Isolation of different online activities.
- Complicated and lengthy instructions can lead to mistakes and insecure tunnel configurations.
- It is difficult to anonymously register and pay for VPN services.
- Certain variables make it likely Whonix ™ / Tor users can be identified. This includes: the hardened network configuration fingerprint, the list of installed packages and those fetched from repositories, the amount of traffic going to one IP address daily (guard nodes), and examination of dropped (invalid) versus non-dropped packets when the firewall is probed. 
For documentation on how to set up a VPN with Whonix, see: Combining Tunnels with Tor.
Where are the Separate Gateway and Workstation Download Files?
The Whonix ™ 14 release introduced unified ova / libvirt downloads. Rather than separate Whonix-Gateway ™ and Whonix-Workstation ™ ova / libvirt downloads, there is now only a single Whonix ™ ova / libvirt which includes both Whonix virtual machines.   The Whonix split-VM design incorporating a separate Whonix-Gateway ™ and Whonix-Workstation ™ remains unchanged.
- New, experimental keyservers have been established which afford protection against this attack.
- The author notes the potential downsides of this attack:
- If you fetch a poisoned certificate from the keyserver network, you will break your GnuPG installation.
- Poisoned certificates cannot be deleted from the keyserver network.
- The number of deliberately poisoned certificates, currently at only a few, will only rise over time.
- We do not know whether the attackers are intent on poisoning other certificates.
- We do not even know the scope of the damage.
- The implication is that traffic might be routinely examined in a high percentage of cases, despite corporate promises to the contrary.
Website traffic fingerprinting is an attack where the adversary attempts to recognize the encrypted traffic patterns of specific web pages without using any other information. In the case of Tor, this attack would take place between the user and the Guard node, or at the Guard node itself.
No comments for now due to spam. Use Whonix forums instead.
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