I just finished with my house mod and now I'm thinking on where I want to place it in the world. I am liking the area near Vivec that is close to both the silt strider, as well as the boat for travel to Telvanni areas. The Vivec mages guild with its guild guide is also pretty close by.

Balmora!
Just kidding. Put it wherever you want to, because there's waaaaaaaaaaaaaaaaaay too much to consider if you're trying to avoid some incompatibility.
If anyone complains, tell 'em to open the CS and move it.

Anywhere except Balmora.

Your best bet is to place it somewhere that it won't conflict with any other mod. (especially any mod that's popular)

Even if this means you have to place it in the Wilderness, you can always set up some fast-travel.

Anywhere except Seyda Neen!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

Spend an hour or two running around ingame. You want to find somewhere thats already fairly flat (cos messing around with Land is.. well i dont like having to do it), and is maybe near whatever resources you need. Ever play Minecraft?

For example: the whole Grazelands region is full of great spots for remote farms/compounds. Got lots of resources near like access to some ashlands, the coast and tonnes of wheat (wheat? ive forgotten the name of that plant. fail). And theres even near-ish cool things like an

if you want to know where there is less mods, look at this ;) => http://planetelderscrolls.gamespy.com/View.php?view=Mods.Detail&id=6000

Just a quick second to Psycolex's advice about changing land. Please don't. Moving a house for a compatibility patch is simple. Dealing with animated grass and water levels and trees showing up in the middle of buildings . . . not fun.

Otherwise, I would just think about the kind of weather and terrain that would suit the feel of your mod. Culture might be a consideration since your neighbors change from place to place. Is the house in the style of any particular Faction/House/race? Just some pointers, you're always free to be a rebel. I've never seen a Telvanni mushroom in Ebonheart, but you could be the one to make it work!

In RoHT, there's a Telvanni Mushroom in Ebonheart.

That would be an interesting screenshot. I've never played RoHT, though I've heard there are a lot of people who love it. See Lorsk, you can put your house anywhere you want . . . I do recommend against putting it right next to a tomb if the tomb has a respawning skeleton guard . . . that can get annoying.

"Honey, I'm going to the market to pick up some kwama eggs!"
"Mind the neighbor, Dear. Ever since he rose from the dead he's been in such a sour mood."
"WHat was that, Honey? I didn't hear you . . . ow! Stop hitting me! Ow! That's it, I'm calling the homeowners' association!"

Are you planning to release this mod? If you aren't planning to release it, put it wherever you want. You're the boss.

If you are planning to release it, I would still say put it where you want. This is a hobby, not a job. You're more likely to do good work if you do it in a spot that inspires you.

But, that aside, as others have said don't make the mistake so many house modders make: do not raise and lower terrain for half a mile in every direction around your house. Follow Frank Lloyd Wright's dictum of molding your house to fit the the landscape. Don't mold the landscape to fit your house.

If you plan to release it and you want to place it in a city, my suggestion is to place it just outside the city limits. Doing so is a nice compromise: you have a city house without the disadvantage of almost certain conflicts. I personally love mods that extend cities outward instead of congesting their interiors. Placing a house outside city walls has the effect of making that city feel larger and its growth more spontaneous. And one more thing: unless you have a good reason not to, use the architectural style of that city. Nothing screams "MOD!" louder than a Daedric-style house in the middle of Balmora.

Your idea of placing it near the Vivec Silt Strider is a good one. There are a few mod-added buildings in that area but it's not nearly as congested as other areas of the game.

I'm curious though: how did you finish a house mod without picking a site?

I built it up in the air above Balmora.

I'm surprised not one person mentioned any of their favorite areas. I'm really just interested in what interesting areas people had in mind for houses.

I ended up putting my house on an island near Vivec.

As mentioned by several, there are already a couple of gazillion house mods that add to Balmora or Seyda Neen. The few house mods I've used are just about all in other areas, because there's a definite shortage of decent housing outside of the heavily colonized SW corner of the island. It was only fairly recently that I found a house mod for Sadrith Mora, and most of the other Telvanni settlements have nothing for the player without killing a current occupant. Locating it along the norther portion of the west coast anywhere above Hla Oad would also be good, as that is also somewhat empty, and the few settlements in the area could use something to make them look less deserted.