1.First of all what known problems may arise during the migration. (Some previous experiences/stories will be helpful)
This is way too broad of a question for any one individual to be able to cover everything, but in my experience what you will need to think about is how you want to handle Exchange going forward since it is built in to SBS, but not built in to regular Windows Server. Migrating Exchange to a standalone installation isn't too bad, but it does cause some headaches.
2.As I know according to the Microsoft KB I need to first prepare the Active Directory with the adprep command. Can this command somehow
cause any problems that will require for us to restore/rebuild the
domain?
This command won't cause problems for you. What it is doing is updating the Active Directory database so it can move up to the new 2008 level you seek. If you watch the command line you can actually see the LDF/MDF files being updated one by one. You will want to do both the domain and forest prep when you do this so your whole forest is ready. ADPrep is pretty straightforward and usually takes less than 10 minutes. It will not cause you to have to restore/rebuild the domain. If it fails, any changes it did will be automatically rolled back, but I have had very little trouble with it.
3.Also another thing that I noticed is raising the Domain Functional Level. Can this thing also cause some problems?
Again, this won't cause problems for you, but you will need to keep in mind that once you've raised functional levels there is no going back; you can't undo it. Now, the reason you raise the functional levels is just as the name sounds, you are moving to a higher version of Windows and thus higher functions/features. It is also so that you can have Domain Controllers running higher versions of Windows; in this case Server 2008 R2. Please note that you will not be able to raise the Domain Functional level past 2003 until all of your Server 2003 Domain Controllers are out of your environment. If you go to raise it and Windows detects a 2003 Domain Controller you will be stopped with an error. This shouldn't be an issue for you though since you are moving from a single SBS to Server 2008 R2.
If you have any further questions I'd be glad to answer them for you.