This 6-3 decision (Justice Stevens joined the majority) was much narrower than it might have been. It dealt only with intangible support given in whole or in part by speech. None of the nine justices questioned the regulation of tangible support (such as funding or arms) which has been the usual "material support" alleged in criminal indictments. So, 100+ convictions will not be affected by the decision.

Here are the definitional parts of the two statutes in question (wording dealt with in the HLP case is bolded):

§ 2339A. Providing material support to terrorists
....
(b) Definitions.— As used in this section—

(1) the term “material support or resources” means any property, tangible or intangible, or service, including currency or monetary instruments or financial securities, financial services, lodging, training, expert advice or assistance, safehouses, false documentation or identification, communications equipment, facilities, weapons, lethal substances, explosives, personnel (1 or more individuals who may be or include oneself), and transportation, except medicine or religious materials;

(2) the term “training” means instruction or teaching designed to impart a specific skill, as opposed to general knowledge; and

(3) the term “expert advice or assistance” means advice or assistance derived from scientific, technical or other specialized knowledge.
and:

§ 2339B. Providing material support or resources to designated foreign terrorist organizations
....
(h) Provision of Personnel.— No person may be prosecuted under this section in connection with the term “personnel” unless that person has knowingly provided, attempted to provide, or conspired to provide a foreign terrorist organization with 1 or more individuals (who may be or include himself) to work under that terrorist organization’s direction or control or to organize, manage, supervise, or otherwise direct the operation of that organization. Individuals who act entirely independently of the foreign terrorist organization to advance its goals or objectives shall not be considered to be working under the foreign terrorist organization’s direction and control.
....
(j) Exception.— No person may be prosecuted under this section in connection with the term “personnel”, “training”, or “expert advice or assistance” if the provision of that material support or resources to a foreign terrorist organization was approved by the Secretary of State with the concurrence of the Attorney General. The Secretary of State may not approve the provision of any material support that may be used to carry out terrorist activity (as defined in section 212(a)(3)(B)(iii) of the Immigration and Nationality Act).
The provisions above were the basis for the majority's distinction between what would be protected conduct using speech and unprotected conduct using speech which could be prosecuted, Holder v. Humanitarian Law Project, Opinion (snips from pp.26-32 .pdf):

We next consider whether the material-support statute,as applied to plaintiffs, violates the freedom of speech guaranteed by the First Amendment. Both plaintiffs and the Government take extreme positions on this question. Plaintiffs claim that Congress has banned their “pure political speech.” E.g., Brief for Plaintiffs 2, 25, 43. It has not. Under the material-support statute, plaintiffs may say anything they wish on any topic. They may speak and write freely about the PKK and LTTE, the governments of Turkey and Sri Lanka, human rights, and international law. They may advocate before the United Nations. As the Government states: “The statute does not prohibit independent advocacy or expression of any kind.” Brief for Government 13. Section 2339B also “does not prevent [plaintiffs] from becoming members of the PKK and LTTE or impose any sanction on them for doing so.” Id., at 60. Congress has not, therefore, sought to suppress ideas oropinions in the form of “pure political speech.” Rather, Congress has prohibited “material support,” which mostoften does not take the form of speech at all. And when it does, the statute is carefully drawn to cover only a narrow category of speech to, under the direction of, or in coordination with foreign groups that the speaker knows to be terrorist organizations.
....
Plaintiffs want to speak to the PKK and the LTTE, and whether they may do so under §2339B depends on what they say.If plaintiffs’ speech to those groups imparts a “specificskill” or communicates advice derived from “specialized knowledge”—for example, training on the use of international law or advice on petitioning the United Nations—then it is barred. See Brief for Government 33–34. On the other hand, plaintiffs’ speech is not barred if it impartsonly general or unspecialized knowledge. See id., at 32.
....
The First Amendment issue before us is more refined than either plaintiffs or the Government would have it. It is not whether the Government may prohibit pure politicalspeech, or may prohibit material support in the form of conduct. It is instead whether the Government may prohibit what plaintiffs want to do—provide material support to the PKK and LTTE in the form of speech.
...
The dissent argues that there is “no natural stopping place” for the proposition that aiding a foreign terroristorganization’s lawful activity promotes the terrorist organization as a whole. Post, at 10. But Congress hassettled on just such a natural stopping place: The statute reaches only material support coordinated with or under the direction of a designated foreign terrorist organization. Independent advocacy that might be viewed as promoting the group’s legitimacy is not covered. See supra, at 18–21.
All of this seems like very fine line drawing to me, although that tends to be the nature of free speech cases.

Lyle Denniston has an analysis at SCOTUSBlog, Analysis: Partial U.S. victory on terrorism:

For the first time in nearly nine years of what the government has called a “war on terrorism,” the Supreme Court on Monday ruled decisively in the government’s favor — but still stopped short of providing an unqualified victory. The Court ruled, by a 6-3 vote, that it does not violate the Constitution for the government to block speech and other forms of advocacy supporting a foreign organization that has been officially labeled as terrorist, even if the aim is to support such a group’s peaceful or humanitarian actions. But the Court added a significant qualifier: such activity may be banned only if it is coordinated with or controlled by the overseas terrorist group. That limitation, however, may be fairly difficult for lower courts to apply case by case; the Court provided little specific guidance.

Conceptually, the ruling in companion cases involving supporters of dissidents in Turkey and Sri Lanka borrowed from a constitutional idea that the Court has used for years for domestic political organizations: the government has less power to control independent political advocacy than it does actions that are coordinated with the political parties. That concept was moved to the global stage, involving U.S.-based organizations or individuals who favor the peaceful goals of two overseas groups blacklisted by the State Department.

The cases of Holder v. Humanitarian Law Project, et al. (08-1498) and Humanitarian Law Project, et al., v. Holder (09-89) are the only war-on-terrorism cases the Court will decide this Term. They involved the federal law that bans “material support” to listed foreign terrorist organizations — the law that is the government’s favorite legal weapon against terrorists.. Although that law is most often used for criminal charges against violent actions or threats of violence, Monday’s decision did not involve that situation. The groups and individual involved do not support any terrorist actions by the listed groups. Rather, they wanted to avoid criminal prosecution for what they considered free speech or other forms of public advocacy to help the listed groups achieve peaceful goals. (much more in article). ....
This case will not have that much impact in the run of the mill "material support" case involving bomb makers, foreign fighters, etc.

Regards

Mike