If I know an upcoming session is going to involve wilderness travel, part of my prep is using things like Mother of All Encoutner Tables from Necromancer Games and the terrain encounter tables in the DMG (both 1E and 3E) to prep a handful of encounters and have them ready.
As the party travels through the wilderness, I have them make checks to avoid getitng lost and I randomly check for encounters at sunrise, noon, sunset, and once for eacch watch they set overnight (usually three 4 hour watches so everyone gets 8 hours of rest). I use a d20 to check and vary what will indicate an encounter based on circumstances (anywhere from 1-4 to 1-12 depending on terrain, time of day, how muuch attention the party is drawing to themselves etc.). If a roll indicates an encoutner will occur, I choose one of the ones I had prepared and use it. Some are strange occurances (weather, sounds, odd magical effect, odd piece of terrain, a ruin, a dragon flying overhead who does not notice them, etc), some are challenges ( a monster, bandits, a pass with a fallen bridge that has to be bypassed, etc.) and some are travelers (a merchant caravan, pilgrims, a hermit, other adventurers, a watch patrol, a ranger, a druid, etc.). If they get lost, it can lead to mii adventures as they discover ruins/mini dungeon crawls, previously unknwn villages, etc.
It allows me a certain control over what kind of encounters take place so nothng will hurt the overall game, but also allows for some randomness and flexibility so that players don't get into the rut of thining everything that happens is relevant to their story or their particular adventure hook they are pursuing. I make sure I have enough encounters ready to cover the length of time they travel, and non-combat encounters can be saved and recycled for use in later treks if they don't get used in the session they are prepped for. Combat encounters that are challenging for the party's current level or specific to terrain are harder to recycle if not used, but may see some later use.
I usually add in an encounter or three along the way that is hook/story relevant as well, so they don't fall into the opposite rut and start thinking nothing that happens inthe wilderness is relevant or important.
I do find that wilderness travel becomes less relevant at higher levels as speels such as teleport, wind walk, planeshift etc. start to become available and get used cutting down on wilderness treks by the PCs. This is one aspect of higher level of play I don't like, as I like the flavor and benefits that wilderness treks bring to the game, but I am looking and trying varying means of curbing the use of those spells without being hamfisted about it.
-M