I assembled this computer with the idea of upgrading the guts (motherboard, CPU, and probably RAM) down the road, while keeping the optical drive, hard drive, case, and peripherals. How much trouble will this cause if I get a similar CPU? How much trouble if I get an altogether different CPU -- like a Phenom to an i7?
Depends who good Windows feels like acting for you. For example at work today I had 2 computers completely different systems. Had to transfer the information from one system to another. I cheated (as such) and just changed the HDD's (effectively same thing, different CPU etc).
One of these systems accepted the HDD and all I had to do was upgrade the drivers and off she went.
The second PC not so good 
Windows was locked in a booting loop. I just reinstalled the OS. I guess I could have loaded into safe mode and tried to repair the OS etc but that HDD didn't have any information on it anyway.
If worse comes to worse and you have a second HDD, you could install Windows on that HDD and just copy over information (if that is what you are worried about) the formation the second HDD and use as storage or something.
Of course (given the forum I posted in!) I won't be installing Windows at all, just using my existing copy of Xubuntu.
Aahh sorry my bad.
Wasn't thinking... for the simple hardware upgrade it shouldn't cause any problems as long as the motherboard will take the CPU you want to add.
But the programs I compiled, will they still run on a different CPU? Will the processor-specific optimizations make them slow on the new CPU, or will they fail to run entirely?
I suggest that you partition your drive (there is a good gui tool in ubuntu) and you copy your home directory on that new partition.
Than you reinstall Xubuntu once your hardware upgrade is done.
Just have to be sure that the new install use only the first partition.