Not all water-based are the same - not all silicone-based are the same - not all oil-based are the same. But in general you can say:
Silicone is great for most uses except you cannot use it for silicone toys - or if you have a sensitivity to the silicone
Water-based works with all toys - but expect to re-apply as necessary
Oil-based is our preference. We use it for all toy materials and use a formulation based on vegetable oils and butters like cocoa & shea butters, almond and vitamin E oils. We have never had an issue with vaginal or anal use - but others have problems.
Try them all and see what you like.