I'm working on some cross-platform desktop application with heavy 2-D graphics. I use OpenGL 2.0 specification because I need vertex shaders. I like 3.2+ core API because of it's simplicity and power. I think that 3.2+ core could be a choice for the future. But I'm afraid that nowadays this functionality may not be available on some platforms (I mean old graphic cards and lack (?) of modern Linux drivers). Maybe, I should use OpenGL ES 2.0 -like API for easy future porting.
What's the state of affairs with 3.2+ core, cards and linux driveres?
Older Intel chips only support OpenGL 1.5. The later chips (since about two years ago) have 2.1 but that performs worse than 1.5. Sandy Bridge claims to support "OpenGL 3" without specifying whether it is capable of doing 3.3 (as Damon suggests) but Linux drivers only do 2.1 for now. All remotely recent Radeons and Nvidia hardware with closed-source drivers support 3.3 (geometry shaders) and the 400-500 series support 4.1 (tesselation shaders).
Therefore, the versions you want to aim for are 1.5 (if you care about pre-Sandy-Bridge Intel crap), 2.1 (for pretty much all hardware), 3.3 (for decent hardware & closed-source drivers) or 4.1 (bleeding edge).
I have vertex and fragment shaders written with #version 120 and geometry shaders written in #version 330, to make fallback on old hardware easier.