We have a similar problem. Are you running diff? That would take forever.

Use something that has associative (hashed) arrays like awk or perl. Assuming you have several files, and an "old" one and a "new" one, that should take less than an hour.
You can search here for examples of both types of code on how to find file differences.

You need a lot of virtual memory, we run on a Solaris 9 sparc v440 with 32GB of memory.
We complete comparing 1.5GB (250K lines) files in about 5 minutes. We do them 12 at a time: 6 old vs 6 new.

I hope this is what you were asking....