I'm a huge fan of the complex non-standard randomly generated encounter that doesn't appear random at all...As opposed the obviously generated encounter, that the party knows is simply a battle to be fought.
In this example, the players should realize that the encounter is simply the result of some random rolling that was done, which is done every day by the GM to determine if an counter takes place. The fact that the Monster Manual was referenced might give clues to insightful players that this was not something in the module (or maybe it was, but the GM wanted more details on the creatures stat block).
In any case, perceptive player would quickly see this as likely not relevant to the story arc, or completing the adventure, and would likely treat this as an opportunity for a few more xp and loot.
The proposed method: While the party is doing their daily Journey Role activities and rolls for the amount of progress for the day, which the players make progress on the Travel Tile. At this time the GM may roll a few times for random events and then determine when they will occur during this day (which hex if during travel), or if it will occur at night time, if so determine which watch. The GM asks the Scout to make a roll when they enter a given hex, followed by a roll from the player who's hero is in the Explorer role.
The party is aware that the Scout rolled poorly, but the Explorer rolled very well. The GM can make opposing rolls (or just roll for the sake of making it look like something). So, in this case the Scout missed the clues that they are entering an area inhabited by a tribe of Bugbear. The Explorer however found a human skull on a stake, who should realize this is an area controlled by some non-human tribe...Further investigation may yield more clues as to what race or even what tribe. Ignoring these signs or not following up by rallying the Scout and Hunters may then trigger a follow-up encounter during the day of travel or the evening during watch.
When/If this encounter takes place is not based on anymore random elements, the fact that they entered a pre-determined hex on the GM's map, or group of hex was the triggering mechanism. Beyond this the GM uses the parties own dice rolls or questions and role-playing elements to determine how to play-out the event.
If the Explorer simply examines it and determines it to be a few years, possibly even decade old, with no visible tracks or trails around it, they may not alert the party...In which case the Scout could be leading the party right into an ambush, or worse be the sole target of the initial phase of the assault. If they Explorer does alert the companions, the Scout and Lookout may get additional attempts to uncover some additional clues, and possibly spot the ambush before they all victim to it. Or maybe the party as a collective decides to skirt the edge of the Bugbears territory.
In any case, this encounter seems anything but random, and gives players much more of a role-playing opportunity. The party would few any encounter as "their fault" for not heeding the warnings, plus the whole scenario plays much more as "part of the adventure", rather than the result of die roles.
For these encounters to play well, it does require a little prep work from the GM. However, the work is not hard, and really only involves rolling the random encounters during the "offline" time that they would be prepping the adventure. Rather than rolling everything at the gaming table, which makes things nearly impossible to not seem random.
The prep work gives the GM time to "Think" about each random encounter that they are creating for the adventure, and even though they may be randomly created, this can simply be use as a skeleton of basic idea of the encounter. It's amazing how much flavor can be put in an initially Random dice roll with only a few minutes of thought.
Additionally, as a GM you can think about how encounters that may have occurred close together actually fit together. This can turn something like a Displacer Beast battle in the morning followed by a band of Gnolls in the early afternoon into, something like: the Displacer Beast was initially wounded by the Gnolls, maybe even have broken arrows in it or claws wounds that are still bleeding, but the beast escaped. Later in the day the Gnolls that were tracking the beast stumble across the party while they are following the beast's blood trail...Or maybe the beast was a pet of theirs that escaped over night and was roaming free, and they were tracking it found its remains and now seek those responsible for killing their animal.
When events "make sense" it's much easier to tie them together or if they don't make sense, than simply ignore the encounter or roll another one. No one has to know, but when your actually randomly rolling right there at the table for everything you may not realize how awkward the events are when played together, and simply go through the motions of another senseless battle, with no gain to the story or campaign.
If an entire evenings random encounter deck is pre-generated then as the GM looking at everything may prompt for additional story arc or side treks between encounters from days earlier, or even changing the order of the encounter may make all the difference in the world as to how the events play out. By placing the lone Druid after the battle with the Giant Spiders, there maybe an opportunity for one of the heroes suffering from the effects of poison to be saved, or wounded party members to be healed, rather than the other way around, when the Druid would be less useful.
The important thing to remember is not to force pieces that don't fit, if something seemed great when you were prepping, but the time is such that the party is running way behind schedule now, and you were hoping to wrap up this arc of the campaign, then its ok to give the party an extra day or more without any encounters for the sake of speeding them along...Or if the party is progressing through the journey much faster than you had hoped, then why not drop in an encounter the was slated for a different location for right now, so long as it works?
To aid me in planning these "Not so" random encounters I've created some rather complex tables, using my own version of the TableSmith application. It basically supports the exact same format, but is much more extensible. Plus, I wanted it to run from a website (thus usable from a mobile device in a pinch) and not as a desktop application, which would require my laptop to be present at the gaming table.
I've got the application working, but I can't provide a link to it here, as I need to find someplace to host it. Once I get this up and running I'll probably write a blog post dedicated to it, explaining its usage, and I'll add a comment here pointing to the other post.
This initial table simply defines the favor of the encounter or event, and this branches off to other tables that further defines the details of the encounter. This large encounter spider web of tables forms the basis of the encounter, and with some thoughtful adjustments like those describes above, will allow randomness of the event seems to be removed. This allow for the dice roles and decisions the players made, essentially determine a starting point of how much initial information they are given about the event that is about to occur.
I have another slew of tables that help me prep for the initial launch of a campaign, which generates a bunch of random tribe of non-humans, a set of powerful NPCs in the area that the players may come to know, as well as a list powerful creatures in the area that may be the source of the trouble that the heroes are tasked to correct.
These lists are randomly determined random tables that I then use as a part of my daily encounters. I also apply large territories for the non-human tribes (that were previously generated), that overlap and assign lair locations to the major creatures and NPCs. This aids in my "Thinking" process as to what is going on when I attempt to inject reasons into encounters.
Of course everything does not require an reason for happening, but it does make for more interesting role playing when the random tables specify results that don't make sense initially, "Orcs of the Black Hand are hunting in the High Moors? But their base is 100 miles away, is this a band of exiles? Are they on a mission for their chieftain? Maybe this is some advanced scouting unit of the band, that is attempting to expand their territories.