Wow - sorry I missed so much on this thread! I completely missed the questions on how I created the Gestalt characters.
I set them up as archetypes of one of the classes. If one of the classes casts spells, that one has to be the 'main' class of the archetype. If not, then I try to use the class that requires the most work as the 'main.' For example, the Druid/Rogue class the OP asked for is made as a Druid archetype. In the editor, go to the Archetypes tab and start a New (Blank) archetype. Use the columns in the center to set up most of the stuff - the race on which the archetype is based, etc. You can add all of the class skills, set the saving throw and BAB progression, etc.
The tricky part is this: most of the classes have 'Primary' and 'Secondary' abilities, and some of them have 'Tertiary' ones as well. You'll have to use the editor to recreate each of the secondary class's primary abilities, re-classify it as a secondary ability and make it available to your archetype. In most cases, this is not really all that hard; it's just tedious. If the original is OGC, it's a simple matter of creating a 'New (Copy)' of the original, reclassifying and making it available to the archetype, save and test. If it's not OGC it requires the more tedious 'Copy/Paste' approach. You'll have to do the same thing for the Secondary abilities if both classes have Secondaries.
The good news is that once you've created them, they're there and available for new class combinations as well. I'd already done the tedious stuff for the Rogue class, so for the most part getting them set up for the Druid//Rogue was a matter of setting them to be available to the new archetype as well as the ones I originally set them up for. In the case of abilities that require a specific level of the archetype, I actually had to create another copy because there's a script that checks for levels in the specific class.
That's about it, I think. These are fairly general guidelines, but hopefully they'll give anyone who wants to make their own Gestalts a place to start. I'm FAR from expert, but happy to help if I can!
There's a script that I had to get ShadowChemosh to write for me in order to make the fighter's weapon training abilities available (thanks, SC!).
PS - I don't have any of the classes set up that have been requested in the last few posts. For the Paladin/Monk, I'd set it up as a Paladin Archetype and add the Monk abilities. I haven't messed with the Gunslinger class at all, so I don't know anything about how they set up the special abilities. Just guessing, I'd say set it up as an Alchemist archetype, since that's the spellcasting class.
PPS - I forgot to mention that (as far as I know) there's still no way to combine two spellcasting classes into a Gestalt using HL.