Since I am a surfactant junkie, I make a lot of bubble baths, body washes, and shampoos that need bottling. I find the easiest way is to get a funnel and pour it in. With a tottle or malibu bottle, I put the bottle into a Pyrex container and then pour it into the funnel. This keeps at least one hand free to clean up messes or get another bottle ready. (I try to have quite a few ready at a given time because once that funnel's full, I gotta move on very quickly!)
I find the bane of my existence is filling lotion containers. I always wait until the lotion has cooled completely before filling the bottles, and it's always a huge mess. I've taken to using piping bags - I have disposable and canvas ones - and I find these work well. I did try to use the cut-a-hole-in-a-sandwich-bag method, but I found I made a huge mess. (But then again, I am a very messy person, so it's not a surprise!)
Again, line up the containers so you're ready, fill your piping bag, and go down the line. I usually fill them up about 3/4, then bang on the table to get the air out, then top it off. This is the annoying part - just as I think I've got a full container, I find another air bubble and have to top it off again!
(If you're selling your products, you might have to weigh them before you cap them off. As I'm just giving mine away or keeping it for myself, I'm not that picky about bubbles or weights!)
I like filling jars...it's so easy! Scoop, bang on the table, and cap.
If you have any suggestions, please comment! There are so many ways to fill bottles poorly, any ideas for doing it well are always welcome!