This is what I do, maybe it will help you...
I created 4 top level folders:
Programs
Contains all my program folders ie 808 folder, 909 folder, etc. I also save the samples with the program. Yes, redundant if I save them in my library already but this keeps everything neat and easy to update, back up and use.
Projects
Contains all data used for projects ie if I am working on a song, I will create a folder titled "Song Name" and everything used for that song will be saved - Programs, Samples, etc
Samples
I use this folder to save all my samples to. If the sample hasn't been assigned to a program or even if it has, it gets saved here first so my library is up to date.
This folder is organized as such...
Drum Machines
Claps
Percussion
Synthetic 2 (NI Synthetic Drums CD)
Sound FX
Vocals
Sequences
Here is where I save sequences. Sequences that have not yet been associated with a project. Basically, if I create some random sequence just to create something, it gets saved here. I use the following file name for easy organization, finding and view in "next seq":
BPM-VERSION NUMBER KIT or
123-002 TR808
Hope this helps.