1. Align Objects. I'd like to be able to snap objects to each other face to face, or center them on various axes... Essentially a 3d version of the align commands in Freehand or illustrator. This would make builds significantly easier to accomplish.
2. Temporary Explode. Let's say I've built an object that has three nested spheres (just for example). If I need to edit the innermost sphere, I have to unlink, move sphere 1, move sphere 2, edit sphere 3, reposition spheres 2 and 1 (without the benefit of the alignment feature suggested above) and hope that I can get all 3 relinked successfully by drag-selecting without accidentally linking the tree in the background.
I'd love to see either a "temporary explode" that moved all of the pieces in a linked object allowing selection of individual pieces, or a way to select interior items with a modified click. The "select individual" function just needs a little more power.
3. Ability to move the position of a "hollow" area. As a quick example, if I have a 10m x 10m wall, I either have to create a huge window to be able to see out of it, or I have to burn additional prims. It would be nice if I could position the hollow area lower on the prim.
4. Make trees count as 1/2 prim.

5. Better lights. I want to do some spotlights that have directional control on them... e.g. architectural lights that shine on a wall, or ceiling spots that illuminate only a small part of the floor... Think art gallery spotlights.
There are a few others I'm forgetting, but these are the ones that I keep wishing I had as I learn this wonderful new world.