"ROMs usually come in DeOdexed, and Odexed.
Odexed - In Android file system, applications come in packages with the extension .apk. These application packages, or APKs contain certain .odex files whose supposed function is to save space. These ‘odex’ files are actually collections of parts of an application that are optimized before booting. Doing so speeds up the boot process, as it preloads part of an application. On the other hand, it also makes hacking those applications difficult because a part of the coding has already been extracted to another location before execution.
DeOdexed - Deodexing is basically repackaging of these APKs in a certain way, such that they are reassembled into classes.dex files. By doing that, all pieces of an application package are put together back in one place, thus eliminating the worry of a modified APK conflicting with some separate odexed parts.
In summary, Deodexed ROMs (or APKs) have all their application packages put back together in one place, allowing for easy modification such as theming. Since no pieces of code are coming from any external location, custom ROMs or APKs are always deodexed to ensure integrity."
this is an excerpt from the rooting guide for dummies. thanx to matlock and akazabam. its their words and not mine.
basically odex roms are smaller but no theming is allowed, but deodexed can be themed.
however, there are certain things that can be flashed to odexed roms, if you want to change the look of it. if you head on over to mik's website you can get most of the mods there.
http://themikmik.com/forums/viewforum.php?f=93&sid=9d1c8ef34bc6a09262ead8da06b5142b