I'm not a FCP guru, but I'd think for a scratch disk you'd do a lot better with a large 7200RPM drive than a Raptor; the Raptor's advantage is more access time than throughput, so I'd think you'd get more benefit from the extra available space on a bigger drive and the fact that you'd be operating with less of it full than with a Raptor.
Either way, FW800 maxes out at a theoretical 100MB/s, while eSATA is going to get you 150MB/s. Since no single drive is going to hit rates like that doing anything but transferring to/from its buffer, there is in theory no advantage of one over the other.
Each has advantages and disadvantages;
FW800 is a little more "smoothly hot swappable" than eSATA;
FW800 is easier to get an external RAID array for--lots of options;
FW800 allows you to use ATA drives in a case;
but...
eSATA doesn't require a bridge board for the drive (maybe cheaper);
eSATA uses SATA drives, which are replacing ATA at the high end, so it's more future-proof.
eSATA is identical in terms of system overhead to an internal SATA disk, while FW800 goes through a seperate bus;
eSATA has no significant risk of frying a port with a bad cable, since it doesn't carry power.
Personally, I prefer eSATA since with a case like those available from Firmtek you can just drop drives into a $20 tray and you're ready to go, plus I can easily use the same case with both my desktop (which has a hot-swap eSATA card) and my laptop. But really, they'll both do the job, so it just depends on which has the features you're looking for right now.