You can also use wooden pipes in some cases (like crossing 2 cobble stone pipes that you want to keep separate for example) as they don't connect to other wooden pipes. Gold and obsidian pipes are the same deal, but they are obviously more expensive and have more important roles to fill.
You can also use Iron pipes sometimes, even if they connect they can still send items different ways that ensure the items stay separate. Diamond pipes can do a similar job and allow you more control, but they are also more work to set up and obviously a lot more costly.
Sand Stone pipes are useful because they don't connect to machines, which will also help you with tight pipe networks around machines.
Maybe I should also look into facades sometime, that could really save me some time thinking about how to (ab)use above properties to my advantage xD If you want stuff to remain visible you can always try using glass facades (there are glass facades, right? xD).
Alternatively, if you have the Additional Buildcraft Items mod there are also Crossover pipes and many other pipes that will help you pack your tubes tighter. The Crossover pipe basically tries to send items in a straight line, so crossing pipes is easy then, even if they are the same type.