Baldy Visitors Center issues permits for the Cucamonga Wilderness, that area that is above Ice House Canyon Trail Head by about 1.8 miles(and has a sign that say's that you do need a permit all other areas you do not), that area is considered Part of San Bernardino National Forest (Don't ask me how they came up with that crap other than the county line separation). The visitor's center will leave you a permit 99% of the time out front on their bulletin board) 95% of the folks never bother - it's the most lax area in Southern Cal.
San J has always been a self-permit (if you are day hiking overnight permits are limited to the spaces available - no one wants to camp on top of another group) at either the ranger station when you get off the tram in Long Valley or both the State Park or National Forest Ranger Station(s) in Idyllwild if the quota for the day has not been met - and it's rare that you cannot find a trail on that side that has an available permit. (The area's outside the State Park are all considered San Bernardino National Forest with the exception of those areas that are Indian Land or BLM Land).
San Bernardino - as in all trails that lead towards San Gorgonio in some shape or form require you to get permits at either the Mill Creek Ranger Station or the other ranger station - they emphasize that they want advanced noticed of at least a week but most folks fax in a request two or three days in advance and if there's an opening they will issue the permit by fax back to you. The Mill Creek Ranger station leaves the remaining permits (unused) out-front each night and you can self-permit if they are available.
Having said all that I've been told on more than one occasion that the reason that the San Bernardino area has a more strict policy is that they want to make the wilderness experience just that and want to limit the number of people per day so that everyone can enjoy the experience as close to pristine as possible (not sure I buy it because if they enter from another trail they sill head for the same area's - typically the Summit or Dry Lake vicinity).
Each area has its own objective and the attitude of the rangers on any given day can change, but it's apparent that the San Gorgonio Wilderness policy tends towards the "militant" at times, not that the other areas don't have their moments as well but they seemed to be less intrusive, more laid back. 95% of the time they are perfect stewards of the different wilderness areas and allow us to exercise our rights to our lands, it's that 5% margin that has made me uneasy when trying to get permits and use the Gorgonio wilderness that has made hiking there uncomfortable at times.
Typically getting a permit is not that hard if you put the effort in. This is for day hiking as mentioned overnight permits are a different story.
These are my opinions based on my experience and it is in no way meant to offend anyone or any rangers as I've had great encounters with all but one and she was none to pleasant about the experience and shame on her for that
