Wipe out a SugarCRM System but Maintain Users, Teams, Roles, and Email Templates. If you want to wipe those elements as well, un-comment the appropriate lines. Note that if you have custom modules or fields, that the custom tables aren't wiped out with this.

sugarcrm_wipe.sql

delete from accounts;
delete from accounts_audit;
delete from accounts_bugs;
delete from accounts_cases;
delete from accounts_contacts;
delete from accounts_cstm;
delete from accounts_opportunities;
delete from accounts_users_1_c;
-- delete from acl_actions;
-- delete from acl_fields;
-- delete from acl_roles;
-- delete from acl_roles_actions;
-- delete from acl_roles_users;
delete from address_book;
delete from address_book_list_items;
delete from address_book_lists;
delete from bugs;
delete from bugs_audit;
delete from calls;
delete from calls_contacts;
delete from calls_leads;
delete from calls_users;
delete from campaign_log;
delete from campaign_trkrs;
delete from campaigns;
delete from campaigns_audit;
delete from cases;
delete from cases_audit;
delete from cases_bugs;
delete from category_tree;
-- delete from config;
delete from contacts;
delete from contacts_audit;
delete from contacts_bugs;
delete from contacts_cases;
delete from contacts_cstm;
delete from contacts_users;
delete from contract_types;
delete from contracts;
delete from contracts_audit;
delete from contracts_contacts;
delete from contracts_opportunities;
delete from contracts_products;
delete from contracts_quotes;
-- delete from currencies;
-- delete from custom_fields;
delete from document_revisions;
delete from documents;
delete from documents_accounts;
delete from documents_bugs;
delete from documents_cases;
delete from documents_contacts;
delete from documents_opportunities;
delete from documents_products;
delete from documents_quotes;
delete from eapm;
delete from email_addr_bean_rel;
delete from email_addresses;
delete from email_cache;
delete from email_marketing;
delete from email_marketing_prospect_lists;
delete from email_templates;
delete from emailman;
delete from emails;
delete from emails_beans;
delete from emails_email_addr_rel;
delete from emails_text;
delete from expressions;
-- delete from fields_meta_data;
delete from folders;
delete from folders_rel;
delete from folders_subscriptions;
delete from forecast_schedule;
delete from forecasts;
delete from fts_queue;
delete from holidays;
delete from import_maps;
delete from inbound_email;
delete from inbound_email_autoreply;
delete from inbound_email_cache_ts;
delete from job_queue;
delete from kbcontents;
delete from kbcontents_audit;
delete from kbdocument_revisions;
delete from kbdocuments;
delete from kbdocuments_kbtags;
delete from kbdocuments_views_ratings;
delete from kbtags;
delete from leads;
delete from leads_audit;
delete from linked_documents;
delete from manufacturers;
delete from meetings;
delete from meetings_contacts;
delete from meetings_leads;
delete from meetings_users;
delete from notes;
delete from notifications;
delete from notifications_audit;
delete from oauth_consumer;
delete from oauth_nonce;
delete from oauth_tokens;
delete from opportunities;
delete from opportunities_audit;
delete from opportunities_contacts;
delete from outbound_email;
delete from product_bundle_note;
delete from product_bundle_notes;
delete from product_bundle_product;
delete from product_bundle_quote;
delete from product_bundles;
delete from product_categories;
delete from product_product;
delete from product_templates;
delete from product_types;
delete from products;
delete from products_audit;
delete from project;
delete from project_resources;
delete from project_task;
delete from project_task_audit;
delete from projects_accounts;
delete from projects_bugs;
delete from projects_cases;
delete from projects_contacts;
delete from projects_opportunities;
delete from projects_products;
delete from projects_quotes;
delete from prospect_list_campaigns;
delete from prospect_lists;
delete from prospect_lists_prospects;
delete from prospects;
delete from quotas;
delete from quotes;
delete from quotes_accounts;
delete from quotes_audit;
delete from quotes_contacts;
delete from quotes_opportunities;
delete from relationships;
delete from releases;
delete from report_cache;
delete from report_schedules;
delete from roles;
delete from roles_modules;
delete from roles_users;
delete from saved_reports;
delete from saved_search;
delete from schedulers;
delete from schedulers_times;
delete from session_active;
delete from session_history;
delete from shippers;
delete from sugarfavorites;
delete from sugarfeed;
-- delete from systems;
delete from tasks;
delete from taxrates;
-- delete from team_memberships;
-- delete from team_notices;
-- delete from team_sets;
-- delete from team_sets_modules;
-- delete from team_sets_teams;
-- delete from teams;
delete from timeperiods;
delete from tracker;
delete from tracker_perf;
delete from tracker_queries;
delete from tracker_sessions;
delete from tracker_tracker_queries;
delete from upgrade_history;
-- delete from user_preferences;
-- delete from users;
delete from users_feeds;
delete from users_holidays;
delete from users_last_import;
delete from users_password_link;
-- delete from users_signatures;
delete from vcals;
-- delete from versions;
delete from workflow;
delete from workflow_actions;
delete from workflow_actionshells;
delete from workflow_alerts;
delete from workflow_alertshells;
delete from workflow_schedules;
delete from workflow_triggershells;
delete from worksheet;