The recommended design for a multi-tier application in a VPC is a three-tier architecture consisting of a Web Tier in public subnets, an Application Tier in private subnets, and a Database Tier in private database subnets. The application should be deployed across multiple Availability Zones, use an Application Load Balancer, Auto Scaling Groups, Multi-AZ RDS, and NAT Gateways for private subnet internet access. Security Groups should restrict communication so that each tier only talks to the tier immediately above or below it.