They might be for a chip on the other side of the PCB, it might be for some high speed serial chip for the PCI-E bus.
If you could narrow down what circuit the caps were from, with a DMM, like a local Vcc supply cap, or part of some RC sensing network like for a step-down regulator, or just a DC blocking cap for some AC signal path. If it was for some near by chip, it might not be that hard to guess a rough value, or find a similar value in a datasheet example circuit.
There's always some risk that more damage could be done I suppose, but you could just try 10nF caps, and see if it runs then. 100nF caps are probably the most common on the whole thing, for all the Vcc lines to all the IC's.
On the 2 GPU's I've tinkered with, there weren't that many sub 1nF caps. Actually iirc one of them is an AMD/ATI HD5770. It's overheating, IDK why, the fan works, but it does make it into windows, before overheating. I've ordered a good Logic Analyzer, but it's stuck in the mail. But yeah now that I know a bit more digital stuff, I look forward to tinkering with that again.
I would try my best to find what circuit it's part of, so what is it connected to, and what are they connected to, then guess a size, but 1 or 10 or 100nF would probably get a lot of circuits working. If needed, I'd solder some thin wire to those pads, then tape or glue the wires down, then go around trying to find, if possible, it might not be, where those caps go.