First off, what's the difference between a linear and a non-linear plot? Characteristically, linear plots will feature a single timeline of events or scenes which the PCs need to resolve one after another in a specific order (e.g scene 1, scene 2, scene 3, etc...). Non-linear plots can have multiple timelines, flash-backs and the scenes do not need to be completed in a specified order, or at all (even though some scenes may be missed out entirely any events in those scenes may still occur).
There's nothing wrong with a linear plot, they're undoubtably easier to write and run, especially if you are a time poor DM, and they can be just as entertaining for players. Here's a few techniques that I've used to make them seem less linear.
Scenario Timeline - One of the biggest drawbacks of a linear plot is that it's easy for players to start thinking that the world revolves around their characters. Using a scenario timeline allows the DM to trigger events independently of the the PCs actions, they might only hear about the event as a rumour or hearsay or over the radio, tv or net, they will still encounter the scenes you have arrange in a predetermined order but they will feel like there's more to the story that they can't influence. Also, If you split your party the timeline can become a useful aid to keeping track of WHEN each group of PCs are rather than WHERE. It's possible to have multiple timelines in operation but make sure that there are key events which tie them together otherwise it's easy for a subgroup of PCs to get too far ahead of the other party members.
Fast Pace - In my experience it's not a good idea to give players too much thinking time in any adventure. When this happens they start reverting to their player archetypes and end up thinking about where their next power-up or wander off trying to find an interesting NPC to chat to. A fast pace to a game often focuses players minds to the immediate task at hand.
Elastic Time - Remember that time is elastic, if you need characters to trigger events and they're in danger of missing it, Dont worry you're the DM, stretch time, but keep up the tension as they race to the next scene otherwise they'll get into the habit of dawdling. If they're on the ball and ripping through scenes like a chainsaw you might need to slow them down a bit by throwing a wandering monsters or random encounter at them. It's a good idea to have a few of this sort of thing in your DMs toolkit anyway, they don't have to be related to the plot, just the setting, a bit like the little old lady who asks the policeman to help her across the road whilst the perp is running away.
NPCs (aka Plot Monkeys) - When a party does get bogged down in a decision it's useful to have a recurring NPC in the plot you can use to prod them in the right direction. I often have an NPC as a member of the party for this exact reason and they also come in very handy when you have a drop-in player that needs a character. Be careful how often you use them though, PCs sometimes take exception to NPCs giving suggestions all the time especially when you have an insecure de-facto leader.
Clues - When you leave clues in a scene to further the plot, make them really obvious. I can't tell you the number of times that a party has walked past a too subtle clue or picked up on it to only miss it's significance. It's an easy trap to fall into when writing scenarios as you become immersed in the plot during the creative process, what seems obvious to you at the time of writing may be a leap of cognitive faith several weeks later when a player encounters it. I often leave multiple clues in a scene which reinforce each other and the correct path to take to the next scene, if the players miss one, they may pick up on the others and players often get a big buzz out of finding clues.
These are just a few of the techniques I use when writing, the important thing is too see what works in your sessions and what doesn't and see if you can improve the player (and DMing) experience. If your players begin to get too comfortable with your writing style mix it up a bit.