The single most valuable item in my garage is the lift I installed last year. It is a two-post, clear-floor, 10,000-pound model from Autolifters. It has been absolutely invaluable in my projects, especially the Lister replica I've been working on. It is a little bit of a hassle to get low cars on it--they have to be lifted with a floor jack first--but the ease it adds to what would normally be unpleasant tasks (transmission install/removal, oil pan removal, even bleeding the brakes) more than makes up for the time spent getting the car on it properly. Drive-on, four-post models would be even more convenient in that respect, but I like having the wheels free so that I can remove them if need be for brake work, etc. while the car is on the lift.
Aside from that, you can never have too much lighting. I've seen garages where there were spotlights installed in the floor to light the underside of the cars, which seems like a neat idea. Having air lines plumbed overhead, to enable you to use air tools all over the garage without dragging the air hose around, is neat, too. A sink and/or parts washers are great additions. I have a "dirty" workbench--where my grinding wheel and drill press are located, and which sits next to my parts washer--and a "clean" one, which I try to use mainly when reassembling stuff that's already been drilled, modified, and cleaned up. Helps keep metal shavings and bits of gasket out of carbs that are being rebuilt.
Also, ventilation is paramount. I have a large (48", IIRC) box fan mounted in the far wall of the shop that I turn on whenever I'm running an engine. I don't have to deal with cold weather much but it does get hot so I keep another large, portable shop fan running at low speed during the hot months just to keep air flowing around the cars, and I also have one of those Portacool swamp coolers that I use on ME when I'm working on something. It's like a portable A/C unit and really helps you keep your cool (no pun intended) when a project is not going according to plan (i.e., all of the time, at least for me).
A stereo is a welcome addition, too, especially when working on something in the middle of the night (as per usual for me, the only time I can get to do my "garage stuff").