I was configuring my BIOS after installing 2 GB of RAM, and I saw this:
I have a 64-bit OS (Ubuntu 9.04 64-bit), so does that mean the motherboard (ASUS M3A78-T) doesn't support more than 4 GB of addressing?

You installed 2 GB and you're wondering if "only" 4 is supported? Strange question.

Are you concerned about the "usable size"? This is most likely video RAM and the space allocated by the BIOS.

If it was me, I would grab a linux distro that has a memory checker like knoppix.net . Next run a memory test. This will give you the allot better idea on the status of the RAM. Most MB only support X many gig, and have flash upgrades. I highly recommend having someone who knows what they are doing to do most motherboard flashes. Seen my share of DOA boards from flashes that went wrong.

I had 2 GB installed and I was installing 2 GB more. Only 3.5 showed up, which should not be the case if the computer is using "64-bit" (actually usually just 48-bit?) addressing.

If you install a 32-bit with PAE kernel, you'll be able to see all the memory also.

No, I think the problem is the video ram.

If I can only address 32 bits, then clearly the 512 MB loss is for the video RAM. But if I could address 48 bits, that wouldn't be a problem. Right?

Or am I missing something?

You have only 4 GB of RAM installed. You can't get more RAM than what you have installed. If the OS sees 3.5 GB, it correctly sees how much is physically available to it.

A single process will have only 2 GB available to it unless you install some kernel patches which move the shared-memory boundary. On the other hand, if you use shared memory (for postgres, oracle, maybe mysql, large virtual ram disk), you can utilize all of the memory currently in your system.

If you want to expand another gigabyte or so, you'll need PAE or a 64-bit OS.