Hard Drive Usage for Speeding up Big Queries

We are trying to optimize our Database server without spending a
fortune on hardware. Here is our current setup.

Main Drive array: 8x 750 GB SATA 2 Drives in a RAID 10 Configuration,
this stores the OS, Applications, and PostgreSQL Data drives. 3 TB
Array, 2 TB Parition for PostgreSQL.
Secondary drive array: 2x 36 GB SAS 15000 RPM Drives in a RAID 1
Configuration: the pg_xlog directory, checkpoints set to use about 18
GB max, this way when massive numbers of small writes occur, they
don't slow the system down. Drive failure loses no data. Checkpoints
will be another matter, hope to keep under control with bgwriter
tweaking.

Now our "normal" activities are really fast. Scanning data, etc., all
runs pretty quickly. What is NOT fast is some of the massive
queries. We have some Updates with joins that match a 100m line table
with a 200m line table. Outside of custom coding pl/pgsql code that
creates the subfunction on the fly (which is up for consideration) to
try to keep the Matching joins to an O(n) problem from the current
O(n^2) one, we are looking at hardware as an option to help speed up
these big batch queries that sometimes run for 5-6 days.

CPU not a problem, 2x Quad-core Xeon, never taxing more than 13%, this
will change as more of our database functions are brought over here
from the other servers
RAM is not upgradable, have 48GB of RAM on there.
Work_mem shouldn't be the issue, the big processes get Work_mem set to
10GB, and if they are using temp tables, another 6-8GB for
temp_buffers. Maintenance Mem is set to 2 GB.

However, the joins of two 50GB tables really just can't be solved in
RAM without using drive space. My question is, can hardware speed
that up? Would putting a 400 GB SAS Drive (15000 RPM) in just to
handle PostgreSQL temp files help? Considering it would store "in
process" queries and not "completed transactions" I see no reason to
mirror the drive. If it fails, we'd simply unmount it, replace it,
then remount it, it could use the SATA space in the mean time.

Would that speed things up, and if so, where in the drive mappings
should that partition go?

Thank you for your help. I'm mostly interested in if I can speed
these things up from 5-6 days to < 1 day, otherwise I need to look at
optimizing it.

Alex