Please consider sharing your modifications with the community and helping integrate them into the standard code!
Subscribe to the freeside-devel mailing list. Send your changes as unified diffs (diff -u). If possible, send changes against current CVS HEAD and also any branch they should be applied to (i.e. FREESIDE_1_9_BRANCH, FREESIDE_1_7_BRANCH). However, if all you have is diffs against a release, well, probably best to send what you have rather than waiting.
Also note that the license requires that you provide source code if you provide hosted access to a modified Freeside instance.
Signup and self-service
You can of course customize the signup and self-service templates as well as plug into the self-service API from Perl, PHP or any other language via XML-RPC. See the FS::SelfService API.
The backend code is structured to make it easy to add "plugins" of various types. You can easily add new price plans, new exports, event plugins (conditions and actions) and new kinds of service tables.
Invoice events have been refactored in 1.9.x and are now just events. The new events have "Condition" and "Action" plugins.
Service tables are fully "plug-in" able - just create the table (see "Schema changes" below) and define the %info hash.
Additional developer information
Schema changes - Quick documentation on how to make schema changes
Agent-virtualized config - Quick notes on how to agent-virtualize new parts of the configuration tables