Well, first of all you should run just the 2GB sticks, you probably don't have XP x64, so the additional GB does nothing except drop your RAM out of dual channel mode. That alone shouldn't cause this problem though.
Did you add the 2nd HDD as a secondary drive, or did you use a disk clone utility to move the contents of the 250GB to the 1TB?
Open task manager, make sure "Show Processes from all Users" is checked, and sort by CPU usage, what is taking up the most CPU. Also, what does it tell you about your RAM, is it full, or do you have some headroom.
Are these the only two things you upgraded?
What is the make/model of your computer. If it is custom built, what is the hardware in it?
Does this slowdown still happen in safe mode?
Have you used a RAM testing bootable utility such as memtestx86+ from http://www.memtest.org/ ?
If you remove the new RAM and HDD, does this still happen? If it doesn't, add the components one at a time, until you can find out what the culprit is.
You need to do some basic troubleshooting before anyone can even begin to guess at the problems you are having.
1Is the RAM the same clock speed and CAS Latency as the original stick? You now have 5 Gig of RAM and now set to single channel (per the config explained above). Is it a 64-bit OS? What kind of spindle speed does the hard drive have? What is the cache? – JFV – 2009-09-05T04:47:25.667
BTW, in general, it's probably best to do a new install anytime you get a new HDD. – RCIX – 2009-09-05T04:54:06.903
1RCIX, there are plenty of disk clone utilities that work fine. Ghost, Acronis, and there are many highly recommended free utilities. I agree that when changing a major component like a motherboard, you're probably best to reinstall, but not a HDD. – MDMarra – 2009-09-05T17:40:05.597