"I Make Projects" has a great how-to posted on creating things in a bottle:
It can be really fun to see what can be made! Jars can be saved and washed, or purchased cheaply at thrift stores. Old toys, plastic animals, fishing lures and all sorts of other things offer great possibilities.
A good talent to develop is what to show and what to cover. Colored or murky water can be used to shadow or otherwise obscure specimens that you don't want seen in too much detail. Strategically-placed labels can cover up bits that don't look quite right. Adding things to the inside of the jar (like sand, rocks, fake plants, etc) can also conceal or highlight things on the inside.
Knowing what to highlight and what to conceal can go a long ways to making a good specimen great! Have fun, and remember that if you don't like how it looks you can always start over!
I think the best part is that the results look great while being amazingly cheap to produce. There's a place for high-end props that take time and money to create, but quick-and-dirty is equally useful.