I've run one home tournament, (which all 16 players told me was very well run), but I have played in dozens of other host's tournaments. I'll give a few thoughts on what works, and what doesn't. Sorry if it's approaching novel length...
- Plan everything in advance! This includes starting stack, blind structure (a topic in itself), rebuys or add-on limits and times, break times and duration, meals/snacks, prize amounts (how many paid, approximate % of total pot for each prize level, etc.), cards, chairs, chips (have the stacks - including rebuys or add-ons - counted out and ready to go), etc. Plan the end time (based on total chips in play, blind structure, etc.)
- Have house rules in place
- When does the next hand begin - when players post the blinds, or when the previous pot winner is declared
- How long can a player wait before making a decision (some players will tank for 5 or 6 minutes if you let them, while the clock runs and blinds increase. Encourage quick decisions - this isn't the WSOP, FFS!)
- Will you race off or round up during chip-ups.
- Are players allowed to look at their phones during a hand
- What happens to the bounty if two players with identical hands knock out a third player
- Have a visible blind timer with an audio alert. The Tournament Director, or Blind Valet are good choices, and you can connect to TVs or laptop displays (multiple displays with an HDMI splitter are better for multi-tables).
- Start on time! Communicate to players when the game starts, and remind them to arrive early so that you can collect money and get people seated. Consider providing an incentive (bonus chips) if they are in their seats on time - late players don't get the bonus.
- Put all of the buy in money into separate envelopes, preferably at the break at the end of the rebuy period. This way you can pay the winners quickly and accurately. Have a separate envelope for bounty prizes, high hand prize, etc.. Have lots of small bills to make payouts easier (hard to have a $35 prize if everyone has bought in with $20 and $50 bills)
- If not every player has arrived, do you start without them and let them join late?
You can let them register late (they aren't considered a part of the tournament until they pay and are seated), or blind off their chips until they arrive. You also need to have a cutoff time so that they can't join after half the player are busted.
Some people consider late registration a bit unfair to other players, as late players have a slightly better chance of winning (especially if other players bust out or get short stacked before they arrive). Others think that blinding off a dead hand gives advantage (free chips) to players at one table over another.
If you do go the blind off route, you need to decide ahead of time what happens if the player is a no-show. Do you remove that player's chips (that haven't been blinded off) from the table, or distribute them to remaining players? When do you do that?
Both late registration and blind off are okay (IMO), and it doesn't really matter which one you choose, as long as you have decided and let everyone know ahead of time. Blinding off seems to be the most common. Contacting late players before the game starts to verify if they are on their way, or still at home watching football, will help to determine if they are merely late getting there, as opposed to unlikely to attend.
When re-buys happen, does the player keep their seat or do you reshuffle the seats somehow? What if they take a short break and get up from the table before re-joining?
That is the difference between a rebuy and a re-entry. With a rebuy, typically they get a stack immediately and stay in their seat. If they want to get up and walk around, their new chips are blinded off. Often bounties are NOT awarded until the final elimination
With a re-entry, the player has to pay a full price (including bounty, high hand, house fee, etc). In that case, the bounty is awarded immediately, and the player can get up and walk around. He is seated in whatever seats are open at the time of the re-entry, which may or may not be the one they were in previously.
Re-entries are a bit of a PITA (IMO), as the tables may have to be re-balanced when the player busts, and then they end up at a different table, which disrupts both tables a bit.
Do you pause the clock during re-balances?(no)
Does play continue during a re-balance? (yes)
I disagree with the No/Yes answers. For your first tournament, at least until you get the hang of things, consider a brief clock pause during rebuys or balances. Don't forget that you will have to finish the hand that you are in, get the chips out, handle the cash, record the bust out, figure out who is moving and to where, etc. Meanwhile a short stack facing an upcoming Big Blind sees the clock ticking away and their stack diminishing in value as the blinds increase while they are sitting there waiting. And if you let play continue while you are doing all that, you would be missing the pocket pair that you have been waiting the last 3 hours to come around

.
Once you have things fully running smoothly, maybe you can process rebuys and balancing quickly and not have to pause the clock (or play), but the first few instances will take some time to do smoothly.
For consolidating tables (as opposed to balancing), absolutely pause both the clock and play.
I'm considering limiting to 1 re-buy per player. Is this wise? Should I let it be unlimited? What are the trade-offs?
The main appeal of tournaments for some players is that they know what their evening is going to cost them before they leave their house. Unlimited rebuys allow players with deep pockets and little regard for the cost a huge advantage. They will go all in with almost any two cards, and end up sucking out on a player who sees their pocket kings cracked by 85o, who doesn't want to shell out another buy in (and another, and another...). The deep pocketed player doesn't see another buy in or three (or six) as a big deal, and someone who just wants a relatively inexpensive evening out will likely find another form of entertainment.
I play in several home tournaments where the rebuy is included in the buy in amount. If you don't rebuy before the end of the rebuy period, it converts to an add-on, usually for 10-20% more than the initial starting stack/rebuy amount. This encourages and rewards thoughtful play, and still allows a bad beat victim to not have to go home early (albeit at a disadvantage to players who get the add on)_
Should I use antes at the higher levels? What affect do antes have on the play?
Antes have the effect of increasing the effective blind amounts, and because there is more money in the pot in relation to players' stacks, it also encourages/forces more action.
Most (actually all) home tournament that I play in don't use antes. You can design the blind structure so that the game has lots of action, especially in the later rounds.
If you do decide to use antes, go the BBA (big blind ante) route. Hounding all the players to throw in their individual antes is a huge time waster.
I'm planning on 200 BB starting stacks, but could do more. Is 18 minutes a good length for levels? I'm aiming for 3-4 hours for the full tournament.
Remember when I said above that blind structure was a topic in itself? Well, were at that point now.
The tournament end time depends on several factors, including blind duration, average blind level % increase, starting stack amount, number of rebuys and/or add-ons, etc. The tournament end time blind level can easily be calculated. The tournament should end very close to the blind level where the BB is 5% of the total chips in play (total chips = 20 x the BB). The total chips will depend on starting stack amounts, rebuys/add-ons, and number of players.
The goal is to design the blind structure so that blinds increase steadily are regularly, with you arriving at the anticipated blind level somewhere near the time that you want to end the game. You need to include some breaks in your structure, and you should probably aim to end about 15-30 minutes early to compensate for the inevitable clock pauses (table consolidation, chip ups, paying people as they leave, processing rebuys, etc.)
200BB is a typical starting stack, but depending on the structure, it can seem like a turbo tournament if not properly thought out. Don't foprget, going from 25/50 blinds to 50/100 (a common staring blind level increase) means that you are at 100BB stacks after just one level. You can have a great tournament with 200BB, 400BB, or even 1000 BB, as long as you design the structure to accommodate.
I'd suggest to try out a few structures on paper (or a spreadsheet), and play around with the % increase, the time for each level, and the starting stack, until you are happy with the duration and the "feel" of the tournament. If you need to increase or decrease the time per level to make it fir, then do so, but for 8 players at a table, you shouldn't be less than 12-15 minutes at a minimum (you want to have at least a full orbit of the table per level). 16-20 is a more reasonable and leisurely pace. If you need to speed things up, consider having longer blinds for the first few hours, then decreasing the duration for the last few levels when the tournament is getting close to ending (there will be fewer players at the table, so you can still get a full orbit even with 9-12 minute blinds)
TL/DR - do a bit of pre-planning! And have a great tournament!