There are definitely differences. The first is that silicone-based lubes can't be used with silicone toys. Water-based lubes can be used with any and all toys (and condoms).
Silicone lubes are (sometimes) slicker and last longer. Especially if you like playing in or near the water (like in the shower). Water-based lubes will wash away in the shower, but silicone will stick around to do its job. Some people feel that since silicone lubes last longer, they are better for anal play than water-based lubes.
Water-based lubes usually don't stain and wash up easily, silicone lubes can stain sheets/blankets/clothi ng and sometimes needs more clean up from your body.
It just depends on what you personally like and what purpose you're wanting to use it for.
Me personally? I prefer water-based lubes, and my favorite of them all is Maximus. It's thick, lasts a long time, and can be used with all toy materials. I use it for vaginal and anal play, and it works great for me! When it dries it just disappears, won't peel off your skin or leave you feeling sticky. (If you're sensitive to parabens, it may not be the lube for you though.)