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I noticed that tournaments like to use scenarios that turn normal gameplay on its head and I was wondering what is the best way to prepare for that...

Things that have come up.
Destroying your opponent's HQ.
Destroying their most expensive unit
Destroying their least expensive unit
Destroying all of one FOC selection (fast attack, elite etc...)
Table quarters

Considering that four out of five of your questions involve killing something, lots of guns or choppy weapons is usually a good idea. Your army by its nature should kill stuff. There is too much variation in armies themselves to gear for killing the things you've listed specifically. It usually comes down to tactics and the choices you make during the game, which is why they were used as part of scenarios.

As for claiming table quarters mobility will help you greatly. Transports for your dudes, jump infantry, cavalry or stuff that deepstrikes will all help you out with that. Make sure you have fast elements to your army.

Most of the things you have listed don't exactly turn normal gameplay on its head. Destroying most expensive isn't hard to remember as half the time its going to be the biggest threat to you so you end up shoot it anyway. Destroying HQ or all FOC is a bit trickier, usually these kind of objectives are secondary/tertiary so usually I would try and seal up the primary before worrying about them (where possible of course) but keep them in the back of your mind and don't waste an opportunity to grab some points when you can. The FOC slot one can be very easy to get against some armies as often if you don't field anything from that slot then your opponent gets that point automatically, hence why I am not a fan of this one. Table quarters are basically objective games (depending on how they actually define the ability to capture etc).

Most of the missions I have seen which actually cause issues are ones which have either created from scratch not been tested enough or are 4th edition missions which people have tried to adapt to 5th (it doesn't really work).

In short the best way to prepare for a tournament is to play as many games as you can against as many different players (ideally decent players though) and lists as you can. If you can get access to them then practice using the missions they will be using in the tournament.

It would certainly depend on your local tournament scene.

I will approach it from my local perspective. I live near Chicago and see a lot of scenario based tournaments.

With these tournaments I often never see the missions before I play them. That said, the best way to prepare for a tournament is to play the scenarios ahead of time. In my case however, I can't

For me, tournament prep comes down to list construction and game day reminders and focus.

List Constuction
for me it is all about minimizing the ways I can be negatively affected by weird rule changes and additions without totally compromising on effectiveness. I would rather be at a minor handicap in all my games then be massively screwed in one game. I can make up small shortfalls with superior generalship, but if your list is completely nerfed there is not much you can do. With the general philosophy out of the way, lets look at some of the variables I consider when building my list.

HQ choice
This is a no brainer, in almost every tournament there is a kill the HQ objective. Its not often the main objective, but it is a common secondary or tertiary objective. With that in mind, I make my HQ durability as high as possible. The best way is with a retinue, but having a squad to babysit is fine too. Spend a few points on terminator honors or that invulnerability save and you will be glad you did.

Troops choice
With nearly all tournaments using objective based missions troops are the most important dudes in your army. You win or lose based on their performance. Do you have enough troop to hold 3 or 4 objectives often for multiple turns to gain points or bonuses. Are you troops resilient enough to hold an exposed objective or defend against an assault

Reserves
Would your list be totally compromised if there was a penalty to reserve rolls or if deep strikes scattered an additional d6. What about if they didn't allow outflanking scouting or infiltrating.

Mobility
How would you deal with a scenario that slowed down your units. Would you still be able to function? Could you contest a far away table quarter or objective?

Unit types
Does your army have a mix of unit types so that a mission special rule doesn't completely nerf it.

Save Denial
Do I have the ability to deny cover/invul saves that may be granted by special rules

All of these should be at least considered on top of basic list building principles like redundancy and ensuring a correct balance of MEQ horde and anti tank weapons. Finally I take into account the local meta game and prepare for basic arch-types of armies. Some examples (Deathwing, KFF mech orks, fateweaver daemons, seer council eldar, drop pod marines, tau, raider spam dark eldar, Air force IG, chimera spam IG, Dreadnaught spam, dual-lith necrons, lash oblit CSM. You should take a few minutes and think about how you would deal with each one of these armies. How would you deploy, would you like to go first or second, what are the dangerous units? Then when you face them you can think back to that 5 minutes brainstorm and be more prepared.

Game day
Get to the venue early and have a look around the tables and more importantly get the rules packet as soon as possible. Ask questions during this period. Then grab a highlighter and go through each mission. What is the primary, secondary, tertiary objective? Are there any bonus points? Are there any special rules for units or terrain? Once that is done, open your eyes and ears. Look at the armies people are getting ready and think back to your brainstorms about how to defeat them and make little mental notes or corrections. Make note of someone talking up their favorite unit. IF you play them then you know which unit to destroy to demoralize them.

Finally, when you are playing constantly ask yourself what am I going to do next. Plan your moves during your opponents turn. Every turn look at the packet to remind yourself of the mission and the objectives.

Good Luck

Razor