Yes you are right. For 99% of uses, 128MB vs 256MB vs 512MB video ram makes no difference. It doesn't make a difference for using Safari, Mail, Office, and most other applications. But for things like graphic modeling (Maya, CAD, etc.), and even gaming, it makes a big difference that you have twice the video ram to store textures.
Penryn brings support for SSE4. Although there probably aren't any programs which take advantage of this now, programs which will will be much faster on Penryn systems then equivalent Merom systems.
Penryn has a 45nm core, which means less heat. Also has a 6MB L2 cache (Merom has 4MB L2 Cache).
Base hard drive is larger.
Multitouch.
New vs Refurb.
If you can nab the MBP with the edu discount, you can get the base model for $1800. The difference is then only $350.