A few suggestions:
If you just want to refine your Eclipse installations with some
common configuration then allow them deviating from that point, you
could copy your workspace folder to all places you want, then switch
to those workspaces from within Eclipse. You can also export your preferences from
within Eclipse using
File > Export > General > Preferences, that may work as well,
If you want to share Eclipse configuration between Ubuntu and Windows, you could install NTFS-3G in Ubuntu, then make Eclipse workspace point to your Windows partition. I'm not sure if Eclipse can deal with this well though (for example JDK path).
If you want to use same configuration for all of your devices and operating systems, and considering you won't be using more than one Eclipse instance at same time:
If you have wi-fi, you could share your Eclipse workspace in Windows then map a network drive letter in the other Windows, and mount a remote network location in your Ubuntus. You could still use second suggestion above for same device.
Alternatively, you could use rsync or similar to synchronize your different workspaces, both when you start and close Eclipse. This way, you move possible performance issues with above option from when you are using Eclipse to when you are starting or closing it.
You sync on start for getting up-to-date with latest changes from other devices, and on close because you want to push the changes you have made to other workspaces as well. In Ubuntu, you could just wrap the sync commands around Eclipse call in a shell script, and in Windows you can do the same with Hidden Start, except that it can hide shell window for you.
You could use services such as Dropbox, Skydrive or Ubuntu One to store your Eclipse workspace and let their client software do the synchronization job for you.
This is what came up to my mind. Maybe Eclipse has something built-in to deal with this other than export wizard, not sure.
What exactly to share
Remember that the workspace is where all your personal configurations reside, including the list of projects you see when using Eclipse. If some of these projects are outside workspace directory you may face path conflicts, for example
C:\MyProject present in your PC but missing in laptop. You could keep all your projects within workspace directory for avoiding this though. Also, if you go for the first suggestion, export wizard as said may work better.
I don't think it's a good idea to share only part of workspace, unless you know what you are doing, and I don't see much benefit from sharing whole Eclipse directory itself (which is not possible between Linux and Windows anyway). You can find out where exactly your workspace is located in
File > Switch Workspace.