Understanding the Requirement: The company needs to migrate applications to AWS, maintaining isolated networks while allowing communication with a shared services VPC and among the applications.

Analysis of Options:

Software VPN Tunnels: This approach involves high administrative overhead and complexity in managing multiple VPN connections.

VPC Peering: While suitable for smaller numbers of VPCs, it becomes complex and hard to manage at scale with over 100 applications.

Direct Connect: Primarily used for high-bandwidth, low-latency connections to on-premises networks, not inter-VPC communication.

Transit Gateway: Simplifies network management by acting as a central hub, allowing easy routing and scalability as more applications are migrated.

Best Solution:

Transit Gateway: This provides a scalable, efficient solution with minimal administrative overhead for managing network connections between multiple VPCs and the shared services VPC.