Legally speaking, there should be a distinction between collective (trade)marks and certification marks. A collective mark (which is probably closer to the existing situation) is where a logo/brand is owned by an "organisation" (nominally NameCoin project) where the "members" typically identify themselves with a level of quality or service, origin, or other characteristics. The problem is that without a legal identity, it would be impossible to enforce the non-usage, for example if a member abused the protocols and was banned/removed as a member. You'd have to resort to courts where common law and thus commercial practices are recognised. Also if it need to be properly lifted up to the point where a certain "quality" is attested by the display of the logo, a register of members or other ways of evidence that the desired association is valid (cf eWallet-scams).
A certification mark is probably the next step where there is a formal set of standards or metrics and the logo can be used by anybody who complies with the standards defined. Currently NameCoin is more a philosophical/ethical "intent" in desiring total decentralisation of the internet with removal of the last central resource with associated tax (aka ICANN et al). In theory the namespace is infinite, in practice we are limited by human memory and some minor technical hurdles in IP address range (until IPv6 is more prevalent). If there is a formal legal owner (anyone who can bring suit in multiple jurisidictions eg EFF) and the certification mark has some value (and can derive side revenue as value-add service).
One way of moving down that 2nd path is to keep the 2D logo for collective mark and have say a 3D version for the subset willing to comply with a more stringent aspect. Give that human time is limited, ideally you'd have some easy way of proving such, whether embedded link, commitment to ongoing compliance, external audit or whatever. Then licensing can be a more formal process with a certain level of assurance.