First, that's the 10th amendment. Second, the Supreme Court tested the 10th Amendment vs the Commerce Clause (which grants the USFG the ability to govern interstate commerce) in Gonzales vs Raich (https://en.wikipedia.org/wiki/Gonzales_v._Raich) and found that the Commerce Clause could cover marijuana sales and distribution (including medical, which was legal in California).

This is totally wrong. Previous Supreme Court decisions, especially Gonzales v. Raich, have set a pretty clear precedent that the Federal Government has the authority to criminalize drugs even when their use is legal in a particular state.

Right, it depends on the judiciary.

But not anymore, because decisions of the U.S. Supreme Court are binding on all lower state and federal courts in the U.S.

only if stare decisis means nothing to them.

stare decisis is not a rule. Moreover, interpretation can and does change over time. The law is not absolute across a given timeframe.

Clarence Thomas agrees with you. The rest of SCOTUS does not.

"The enumeration in the Constitution, of certain rights, shall not be construed to deny or disparage others retained by the people."

I don't think this means what you think it means. A quick glance at wikipedia expands and explains:

The Ninth Amendment explicitly bars denial of unenumerated rights if the denial is based on the enumeration of certain rights in the Constitution, but this amendment does not explicitly bar denial of unenumerated rights if the denial is based on the enumeration of certain powers in the Constitution.

What unenumerated right is being infringed here?

One could suppose the right you're referring to is that of the individual states to create their own laws...except the Constitution covers that one in Article VI, clause 2:

This Constitution, and the Laws of the United States which shall be made in Pursuance thereof; and all Treaties made, or which shall be made, under the Authority of the United States, shall be the supreme Law of the Land; and the Judges in every State shall be bound thereby, any Thing [sic] in the Constitution or Laws of any State to the Contrary notwithstanding.

Or the right of the states to regulate trade...

[The Congress shall have Power] To regulate Commerce with foreign Nations, and among the several States, and with the Indian Tribes;

...hmmm.

The problem is that a) weed is illegal in the United States under the Controlled Substances Act (CSA) (21 U.S.C. § 811) b) the President of the United States has decided not to enforce this law (in violation of Article III clause 5: "he shall take Care that the Laws be faithfully executed"). This had led to a murky situation where the laws that apply to a local company are very very different from the laws that a multinational entity like Microsoft has to worry about. I'd be very interested to see what happens in the long run here.

I'm pretty sure there are federal laws against aspects of the marijuana industry which have been long enforced by the judiciary.

Shipping it across state lines seems like an obvious example.