We were able to get all the lists for a "site url" using the Lists web service GetListCollection operation.
In the list-collection we were able to get all document libraries using the attribute Server-template=101.
But we were not able to differentiate the user defined document library and default SharePoint document library.
Sample Response:
User Document Library:
<List DocTemplateUrl="/Shared Documents/Forms/template.dotx"
DefaultViewUrl="/Shared Documents/Forms/AllItems.aspx"
MobileDefaultViewUrl="" ID="{CCA12CD0-6049-4D4E-9AC3-0D72DDED8A55}"
Title="Shared Documents"
Description="Share a document with the team by adding it to this document library."
ImageUrl="/_layouts/images/itdl.png" Name="{CCA12CD0-6049-4D4E-9AC3-0D72DDED8A55}"
BaseType="1" FeatureId="00bfea71-e717-4e80-aa17-d0c71b360101"
ServerTemplate="101" Created="20130404 04:20:02" Modified="20140211 05:47:33"
LastDeleted="20130404 04:20:02" Version="0" Direction="none"
ThumbnailSize="" WebImageWidth="" WebImageHeight="" Flags="4104"
ItemCount="14" AnonymousPermMask="0" RootFolder="" ReadSecurity="1"
WriteSecurity="1" Author="1" EventSinkAssembly="" EventSinkClass=""
EventSinkData="" EmailAlias="" WebFullUrl="/"
WebId="cf0491db-4c74-4beb-a5bc-628f5dfc77be" SendToLocation=""
ScopeId="5635aa9e-6a65-4f26-9d2d-433b7a01b8e6" MajorVersionLimit="0"
MajorWithMinorVersionsLimit="0" WorkFlowId="" HasUniqueScopes="True"
NoThrottleListOperations="False" HasRelatedLists="" AllowDeletion="True"
AllowMultiResponses="False" EnableAttachments="False" EnableModeration="False"
EnableVersioning="False" HasExternalDataSource="False" Hidden="False"
MultipleDataList="False" Ordered="False" ShowUser="True"
EnablePeopleSelector="False" EnableResourceSelector="False"
EnableMinorVersion="False" RequireCheckout="False"
ThrottleListOperations="False" ExcludeFromOfflineClient="False"
EnableFolderCreation="True" IrmEnabled="False" IsApplicationList="False"
PreserveEmptyValues="False" StrictTypeCoercion="False"
EnforceDataValidation="False" MaxItemsPerThrottledOperation="5000" />
Sharepoint Default library:
<List DocTemplateUrl="/SiteAssets/Forms/template.doc"
DefaultViewUrl="/SiteAssets/Forms/AllItems.aspx" MobileDefaultViewUrl=""
ID="{395CA397-5A05-4F46-A287-D8C593746A60}" Title="Site Assets"
Description="Use this library to store files which are included on pages within this site, such as images on Wiki pages."
ImageUrl="/_layouts/images/itdl.png" Name="{395CA397-5A05-4F46-A287-D8C593746A60}"
BaseType="1" FeatureId="00bfea71-e717-4e80-aa17-d0c71b360101"
ServerTemplate="101" Created="20130404 04:20:01" Modified="20130404 04:20:02"
LastDeleted="20130404 04:20:01" Version="1" Direction="none"
ThumbnailSize="" WebImageWidth="" WebImageHeight="" Flags="4104"
ItemCount="0" AnonymousPermMask="0" RootFolder="" ReadSecurity="1"
WriteSecurity="1" Author="1" EventSinkAssembly="" EventSinkClass=""
EventSinkData="" EmailAlias="" WebFullUrl="/"
WebId="cf0491db-4c74-4beb-a5bc-628f5dfc77be" SendToLocation=""
ScopeId="5635aa9e-6a65-4f26-9d2d-433b7a01b8e6" MajorVersionLimit="0"
MajorWithMinorVersionsLimit="0" WorkFlowId="" HasUniqueScopes="False"
NoThrottleListOperations="False" HasRelatedLists="" AllowDeletion="True"
AllowMultiResponses="False" EnableAttachments="False" EnableModeration="False"
EnableVersioning="False" HasExternalDataSource="False" Hidden="False"
MultipleDataList="False" Ordered="False" ShowUser="True"
EnablePeopleSelector="False" EnableResourceSelector="False"
EnableMinorVersion="False" RequireCheckout="False"
ThrottleListOperations="False" ExcludeFromOfflineClient="False"
EnableFolderCreation="True" IrmEnabled="False" IsApplicationList="True"
PreserveEmptyValues="False" StrictTypeCoercion="False"
EnforceDataValidation="False" MaxItemsPerThrottledOperation="5000" />