The first thing your lair's terrain will do for you is provide concealment. Anyone looking at the thing from the outside should be unaware that a lair is hidden there. This is what makes underwater and underground lairs so popular, despite the engineering difficulties. That said, you can use partially collapsed caves, mine shafts, or similar terrain features if you don't want to go entirely underground or do a lot of digging.
Lairs are as individual as their owners so I can't give very specific advice. However, I'll tell you about the most interesting general tips I've found over the years.
- Urban decay is a hard phenomenon to reverse. Once a building is abandoned, it often stays abandoned unless some large-scale redevelopment money is poured into the neighborhood. For this reason, abandoned buildings - most often large industrial structures, like power plants or factories - are popular for lairs on the cheap. Detroit is often the default destination for new villains who are working in Ontario because it's a mess, but every city has its share. You'll have to worry about adventurous photographers, because these sorts of buildings are a magnet for any yahoo with a camera who's already had his tetanus shot.
- Subway tunnels in the largest cities have a similar abandonment problem, and they give you easy access to transportation into the bargain. You run the risk of snooping city employees here, though, so you'll have to arrange some kind of cave-in to block access.
- With enough money, you can sometimes snap up an entire tenement building. The people selling such things don't usually investigate the buyer too closely, as long as the money is good. You will have some overhead keeping the city happy, since theoretically you are the owner of a residential building, and must pass inspections and other bullshit like that. Only do this if you are confident you can bribe your way out of inspections as a rule.
For villains with control over water, earth, metal, or similar useful elements - or just those who can move such things around with their other powers - a lair can be placed almost anywhere. If you are one of these people, consider yourself lucky. Even if your power isn't on that list of elements, you can be creative.
Take two villains, for example: Mountain Man and Tokyo Rose. Mountain Man lives in a wooden cabin, but his control of rock lets him move that cabin anywhere in the mountain range where he lives. Rose has plant control - she can infuse plants with Stage 2 superpowers, which includes mobility and non-metabolic growth - and she lives literally in a huge tree that she keeps growing underground. She sends tendrils up to break through the street or into buildings, and she literally steps out of a giant blooming flower. Stylish, that one.
Size and Layout
You should make a list of your typical activities. Planning capers will want its own area. Record storage, if you're into that sort of thing, needs its own area. You should budget at least 1500 to 2000 square feet for these things. Another 150 to 250 square feet will account for a kitchen and pantry, if you need to eat. The typical remodeling cost for a house assumes a 10x10 kitchen, and you want to include storage and a dining area as well. You'll want a place to sleep, so decide how big you'd like that to be - 200 square feet is more than adequate, but some villains prefer much more expansive sleeping quarters.
Plan for recreational use too! You'll often spend hours or days in your lair lying low, so you need something to entertain yourself. A gymnasium, library, or den - provided you don't get too attached to the contents - is perfectly appropriate.
You could theoretically build a lair on the Moon - Apollo did, after all - but that's not super helpful if you want a short commute to your crime scenes. For this reason, you should make sure that your lair is easy to get into and out of, and make sure you are close to the places you want to be. The longer you're moving from caper to lair, the more chances the cops have to pick up your trail. Conversely, a lair right underneath your major crime scenes will be discovered pretty fast as the cops search the area after you hit them.
Make sure your lair can't be found by a simple process of triangulation. What do I mean by that? Let's say you are too lazy to travel far - say, 10 miles at most - for all your capers. Pretty soon your crime spree looks like a big circle on the city map. The cops are going to rightly conclude that there's a moron villain somewhere at the center of that circle, and go looking for you.
Your lair will ideally be somewhere on the fringes of your activity area. Try to vary your travel time so that the lair isn't too far away (nobody wants to haul swag for three hours), but not necessarily within the borders of your preferred turf. Diligent villains keep a map showing past crimes using push-pins or permanent ink, and will look at it when planning their next caper.