In Secret Invasion, the 100 point Fantastic Four were unique. Since then, there have apparently been three separate starters including them. In the Classics starters (Fantastic Four Vs. Mole Man, and Fantastic Four Vs. Doom) the figures weren't unique. If for example you were to use SI #104 The Thing, could you also use one or more CL 1-11 The Thing on the same team?

On a separate note, any clarification as to which versions were or were not unique, and which starters they would be listed in with which set number would be very helpful.

I don't have the figures in front of me, but looking at the Units section here on the realms, none of the Fantastic Four figures you mentioned were unique. However, if they were, they would only prevent you from playing another one with the same name, the same set symbol, and the same collector’s number.
If you have a Mr. Fantastic from the starter set and one from the classics pack, they would share the same name, but have a different set symbol and collector's number. So they would not count as the same character for force-building.

Going by the units search engine, it shows SI #101 Mr. Fantastic as unique. Note the silver ring around his base. While his Classics version has no silver ring. The confusion comes from the fact that at least one of the starters has the four miniatures listed as their Secret Invasion set numbers, but not being unique. Again, any clarification on which starters have which pieces listed as coming from which set, and whether or not they are unique in them, would be great.

The "Mr Fantastic" you link to from SI is actually "Reed Richards" a seperate figure, a LE version from the set, NOT available in the starter or Classics packs. AFAIK, no version of Fantastic is unique. Duplicates abound!

The only unique in the Fantastic Four starter was Dr. Doom. They do have the Secret Invasion set. Symbol. There are prize figures of the Fantastic Four that are unique however. They used the same sculpts. Look for The Thing with Yer ever lovin, pal. That is the starter one, which is not unique.

And BTWs, the pictures of Human Torch and The Thing show the Johnny Storm and Benjamin Grimm versions, respectively. This is an "error" on the Units sections part. You can read the name of the figures in question. Incidentally, the Victor Von Doom shows the Dr. Doom image. In these cases (and most), go with the information given, rather than details in the image.
(I put "error" in quotes as it's perfectly understandable to use one picture for duplicate sculpted figures, IMO, but in this case some variances are indeed visible. C'est la vie.)

Ah, I see. I missed the figure's name on the dial, my mistake. I assumed the figure shown would be the one listed, that's what I get for assuming. Thanks for the replies and the clarification.

No problem man. Never feel bad for asking, there's always worse out there (whether it be dumber, more abuse-ridden, been asked to death, etc).

#101 is the Vet Mr Fantastic
#111 is the LE Reed Richards, a unique.

Go by the background color on the picture of the specific card. You can use multiple #101, or the same figure, but from the different sets you mention.

That's all well and good when the fig is in hand. But in this case the information was derived from the units section, and seemed genuine. Once you blew the picture up (and knew to check the name) that changed things slightly.