Skipping the session scoped issues you're bound to enjoy I'll focus on less common code level strategies.
You will have 2+ isolated application scopes. This creates challenges in synchronicity. Examine the app code for writes to the app scope. Should some condition require updating an app scoped value, that value must be reflected in all sibling application scopes.
Know that each instance will have its own onApplicationStart() & onApplicationEnd() events. Depending on what happens in the code, it could cause mischief.
Be aware of things like FuseBox (framework) when load balancing. FuseBox generates files locally that are not replicated on other server instances.
When logging, emailing errors, etc., use an instance identifier so you'll know which server you're working with.
Should your app need the originating IP address of a request, you may need to enable X-Forwarded-For HTTP headers within your load balancer. Otherwise, you could get the IP of the load balancer on every request.
Verify Identical on EACH Instance:
- Security implementations
- ColdFusion & Java versions
- Datasources
- Mappings
- Virtual directories
- Shared resource locations ..
- CF Admin settings: site-wide error handling, etc.
- CF account privileges, Important!
Consider using the ColdFusion Server Manager to assist consistification. ;)