@jimp:
pfSense logs are only stored in /var/log, not "all over the place". There may be some packages that break that convention but they are the exception, not the rule, and the packages should be fixed if they are doing that (where possible), or at least under /var/.
A custom install allows for creating multiple partitions and such, though using a second disk isn't so simple. We have plans to revamp the installer soon, so that might show up, but it's too soon to say.  For those that need/want to use a second disk, formatting and adding it to fstab is fairly easy for the technically inclined.
What I meant for "All over the Place" was in the GUI. You have to click around through some of the different functions to find the logs. My suggestion; which is still valid by the way, is to move the log directory to a secondary disc that has a catalogued files system specifically for logs and create a central location in the GUI to manage and clear ALL logs.