For stuff I really want to keep from leaking I use 3M 5200. I've used it below waterline in the boats when I have to and it's stayed good for years in salt water. It is spendy and doesn't come loose easily. I think 3M makes a "dumbed down" version that isn't as tough to get loose but I've never used it.
For stuff that's not as critical I use DAP Kwik Seal Plus (Kitchen/Bath Adhesive Caulk) or for bigger gaps/bigger jobs DAP Alex, Alex + or Dynaflex. Like the latex stuff because it's paintable and it and other stuff will stick to it. Easy to apply and water clean-up too.
I don't use silicone any more 'caus I have trouble even getting more silicone to stick to it much less anything else.
I used this for resealing the water heater when I reinstalled it. I also used it on the roof when I replaced the screws. It is an adhesive / sealant. It sticks very well, but not like the 5200. I also like the idea of UV protection for exterior work, and it has held up very well. I like white color sealant. I've noticed silicone sealant attracts dirt and doesn't work as well for me.
Someone on this forum also turned me on to Dicor products. Our local RV dealers stock them and they are used extensively in the RV industry. You might check them out and see if they would work for your application.
If you are close to a Camper World, they sell a great one called "RV Sealant". Dont have the number of it now, but it is great, but sticky. Sorta pricy, about $7-8 per tube, but it works great.