Thankfully, my bad feeling was off-base. According to Speaker Pelosi's summary of the conference committee version of the stimulus (word document here), the NSF will end up with $3B, DOE Office of Science gets $1.6B, there will be an ARPA-E with $400M, NIST will get $580M, NIH will get $8.5B (more than the entire NSF annual budget, by a good fraction) for research and an additional $1.5B for university facilities; and NASA will get $1B, with $400M of that targeted for climate research.
Now all they have to do is actually pass this thing.
I know that many people out there have philosophical objections to this kind of investment being done in a stimulus bill (as opposed to a regular appropriation). I also know that big one-time spikes in funding can be disruptive and harmful in the long term. Still, this is the first decent investment in the physical sciences in years, and it's hard for me to feel misgivings about it given that we've given more than TEN TIMES the total up there in taxpayer dollars to prop up just AIG.