Note: This is just how I work, and I don’t profess to know what’s best. Perhaps seeing how I use software will help you, perhaps not. If you have another technique that works for you, go ahead and share it!
I launch applications in Mac OS X in three ways: from Alfred, from the dock, and with keyboard shortcuts set up in BetterTouchTool. This may seem inefficient, since I have to choose what to use each time, but generally, I use the same method for each specific app, so it doesn’t waste any time. I keep my default dock minimal: Finder, Google Chrome and Plex. Plex and Chrome are usually launched from the dock, and I use it to switch between open apps (I really need to get comfortable with the application switcher though, as I’m sure I could save time). I launch Notational Velocity with a keyboard shortcut: Command-Option-N (and I bring up Jumpcut with Command-Option-V, a natural companion to Command-V). For everything else, I use Alfred.