(Titled this generally so other people can use this thread as well...)
So a player of mine re-invented Conjuring the Mystic Tower using experimentation and received a major side benefit. Now I'm left to come up with something, and in order to get some inspiration, I thought I'd ask for some suggestions here. 
So, any ideas?
Some suggestions from the tiop of my head.
1- The tower looks mundane. Weathered, the surface looks like it is made by individual stones put together instead of as a single chunk of rock, etc.
2- The tower has a much wider basement than the normal tower
3- The tower can be built anywhere and it remains there, regardless of the support it gets. So it can be cast on water and it will remain still in the middle of the ocean. Or it can be cast on a rooftop and it will not crash down the building below. The only place where it does not stand still is in mid air since it needs a suport, however flimsy. It might stand on a cloud though, who knows. (this is the most extreme case, and might not qualify as a major side effect; I was going for a Rego side effect)
4- The tower also develops stone foundations,so it cannot be tunnelled.
5- The tower can be redesigned in every casting, so rooms, number of floors, where is the entrance, how many and what form the windows have...
6- The tower has all the furniture and Herban stuff with no need of requisites
7- Casting the spell costs 1 or 2 pawns of vis less.
Cheers,
Xavi
One source for variations due to experimentation are the Character's Virtues and Flaws. Their magical (and to a lesser degree, mundane) V & F can be reflected somehow in the final product.
The simplest is to look at the spell, and decide if there are any "house-ruled" limits on it, and relax those limits. For instance, with CtMT, there is the question of the "foundation" - the "20 feet" set into the ground. Some players assume this is a "basement", 2 underground stories, but that is really not a "foundation" - but with a side benefit, maybe it would be.
Other benefits might mimic an additional Art - decide what Art to add - maybe the tower is always heated/cooled, maybe it is pre-lit (to a small degree), or maybe it has a cistern on top for running water. Maybe it is more ornate than expected, or more complex (secret passages?). Maybe the "Living Conditions" are an additional +1 for any who sleeps there. Maybe the room are all perfectly formed, giving any lab a +1 bonus from the shape of the room (ala the Laboratory chapter of Covenants).
Heh, cross-post - see spell description for specifics on any "basement" and "foundation" in the spell-as-written.
The tower is gilded in gold.
The tower is warm in the winter but cool in the summer +1 living conditions.
The tower can be built on any surface at any angle and it won't fall over or crush what it's standing on. If the surface it's standing on falls over or is destroyed the tower comes down. In a big tree, sure just built wooden platform to cast it on. Straight out of the side of a cliff, why not? But living in it will be tricky and you'll want to shutter the windows on the wall that's now the floor. One on top of another till you reach the lunar sphere. Umm okay but your going to need...let me do the math...a royalcrapton of vis. Also you can't build it in midair. Also don't let anyone knock over the bottom one. Edit-hadn't noticed xavi's post.
The tower can move very slowly, like a giant wadding through mud.
It's fully furnished.
From the outside no windows. From the inside windows. Weird.
Two Words "Disco Ball"
Somehow, the tower captures the platonic idea of the perfect tower. It's a subtle but powerful effect on any visitor. +3 to lab aesthetics, and +3 to any roll to impress visitors.
The tower can be "grafted" seamlessly to other pre-existing buildings, tunnel systems etc.
Somehow, the tower is twice as spacious inside than it looks outside.
Side effects that don't effect the tower.
The caster get's a +3 bonus to stamina for moon duration. If wizards communion is used only 1 participant get's the bonus (chosen at random)
The caster ends up garbed in a full suit of Plate Armor. If wizards communion is used all participants get a free suit of Armor. (Or maybe it's swords, or jewlery)
The ground around the base is seeded with some random metal ore or type of gemstone.
The the land within sight of the top, up to a standard boundary size, is made more fertile.
A minor magical aura (1-2) forms in and around the tower. It does not add to another magic aura and is easily overpowered by foreign auras.
The tower does not grow upwards, but sideways to end up as a BIG wall with living quarters in it.
Some interesting stuff so far, some ideas that also crossed my mind. Just as a reminder: I'm looking for a major side benefit. Here's the example from the book (emphasis added):
The tower includes a shrouded glen effect, meaning only those whom the original participants WANT to be able to find it can find it.
The tower comes with its own earth elemental guardian
The tower is in a awaken state
The tower is formed in a regio
The tower grants the details taught by the participants at the time of creation
The effect can also restore buildings
W
The tower acts as a preternatural tether (with a tether score of 1) - see RoP:M, p.8-10 - which in many cases will increase the local Aura by 1. This may be somewhat too powerful, so you can assign the event only a relatively small chance of taking place (say, 30%) on each casting.
What's his sigil Toa? I like to tie them in.
Marble. He is a Rego Terram craft magic specialist, and his spells tend to leave marbled surfaces or stuff he creates might just be plain marble.
1- The top of the tower generates Auram Vis during the autumn storms/winds or Terram Vis can be found in the basement
2- The tower becomes famous as the pinacle of Architecture, using styles of building Instead of the standard romanesque building that is common, the tower becomes more gothic (think Notre Dame cathedral in France with Wall-sized stained-glass windows). A style that is starting to appear in the 1200's but this tower puts even the gothic buildings to shame. This is the type of building that 21st century architects will gawd at. And thus, Architects and others will come to the tower and offer to study it and in return will occasionally give him books in Artes Liberales and other mundane skills to his library
3- The Tower is built through the ways of sacred gemoetry (from AM4 Mysteries) and will grant +1 quality when writing books inside or +1 quality when study, becuase of the light and everything is alligned with the moon, sun, and the ley lines etc.
4- The tower attracts a housegnome that will automatically repair damaged things and give him an opperunity to build flawless tools & ingredients for his lab
5- He gets a fully equipped lab with 3 refinement levels already built into the tower at creation.
6- he gets a circlular wall with battlements around the tower as well.
1- The tower possess a rainwater system and makes stranger sounds but it's healthier (one lab bonus could be +1 Health or Upkeep but -1 Aesthetics or Safety)
2- The tower slowly changes its orientation in each season (+1 Muto, +1Health, -1 Safety)
3- The tower knows who lives inside, blockin their doors and windows to strange people.
4- One Mouse of Virtue bring for the basement.
5- The creator can open and close any door in the tower with one Perception + Awareness against 9 bor the Stealth total achieved by the intruder.
The latter is easy enough to exaggerate - it's not just "marble", but highly polished, truly impressive marble, etc etc. And perhaps easily changed in color to all the varieties marble comes in. Such an artwork would be highly prized among some magi, and impress the pants off visitors.
But perhaps that's not "major", or not by itself. And yet, you don't want to give too much away - but that depends on your saga.
+1 Living Conditions is fairly important, especially to old(er) magi.
+1 general bonus to labs is big too, and something many magi willingly spend a couple seasons to achieve. This would be from the mystic shape and balance of the rooms, etc.
You could toss in a "special lab bonus" on any activity involving Rego or Terram - studying, studying from Vis, writing about those Arts, teaching those Arts, and any and all lab activity involving them - the size of the bonus is up to you.
You could combine several of those, until you feel something fair and "major" is achieved.
Or, you could go a different way - perhaps the caster has an innate "connection" to the Tower, a sort of Intellego aspect to it, and, if touching the tower, can take an action to "concentrate" to sense who is in the tower and where. Details up to SG (things like this can often be better left imperfectly defined - it comes and goes).
Perhaps with respect to the Rego part of the mage, the caster can, with concentration and slowly, over an hour or a day, alter the tower's configuration. This could create sealed chambers, modify rooms and floors, combine or split rooms, etc., as needs change over time. (Perhaps scale the speed to the size of the change, so a cubbyhole or a small window could be opened and sealed fairly rapidly, but smoothing the main staircase into ramp would be a bit slower, and changing the main stairs from clockwise to counter-clockwise might take all day, etc.)
(A more extreme version would allow the tower itself to move over time - not sure I'd want to suggest a "walking" tower, but one that can move slowly, a (few) hundred paces overnight, just slow enough that it can't actually be seen as it happens - that could be fun.)
Or, with regard to the Terram part, perhaps she could mix and match the material of the tower to stone/glass/metal (within reason?)?
Also note that this spell can be taught to others - if the "major side benefit" is good enough, Duremar will want a copy, and in a generation or two, everyone who learns CoMT will have this major side benefit.
...if you let them know about it. 
This is something that the rules have never clarified (and I wished they had): whether you can "pass on" what you've gained from your experimentation.
After a long debate, in our troupe we decided that no, that's not the case, since whenever you learn a spell from a lab text you are effectively learning the spell ex novo (and thus are subject to the same limitations that you'd have without the lab text -- it's just that the lab text makes you work faster). Then there was another long debate about whether you could transfer such an "experimental" spell to a casting tablet, and I really do not remember how that went 
Oh, really? I assumed it was "part of the spell" that you ended up creating - that is, the side effect itself is now embedded in that version of the spell, and could be taught as such.
What it sounds like you're saying is that any side effect (good or bad) is completely within the mind of the individual that creates it - and that the lab notes, were someone else to look at them, merely show how to create the 'standard' spell, rather than the version you created.
I do admit, that simplifies the question of "why aren't the standard spells that magi learn all the experimental versions?" ...answer: "because you can't pass on experimental lessons. You can only pass on Insights, which are a different game mechanic."
There's several references to it being possible to include the beneficial side effects of experimentation in the Colentes Arcanorum sections on folios in the Bonisagus section of HoH:TL. For instance, in the Example Portfolio section on page 23, it says:
"The Lab Texts were chosen because the inventing magi used experimentation, and each spell has a beneficial side-effect."