At my day job I'm the Deployment Architect for a Fortune 50 company with an SCCM 2007 environment ( currently migrating to SCCM 2012 ) that has over 300,000 clients. Here's a few tips.
1) We don't do Per-User installs. They are impossible to manage and report on. If an installer must have Per-User resources and we can't get the application (typically vendor provided) we do this using an Active Setup technique where the first time each user logs on the MSI does a repair and populates the Per-User resources. Just realize you'll never get it off... it's essentially forever.
2) SCCM can handle non MSI deployment types but well written MSI's work the best.
3) Use snapshotted VM's to test your install in the SYSTEM context. (PSExec is your friend)
4) Test your install, uninstall, reinstall, upgrade, repair, change. Make sure everything is bulletproof.
5) Don't wrap up prereqs into a setup.exe bootstrapper. Decompose it and allow SCCM to package each of these items. You can then use package chains, task sequences or application model to allow SCCM to manage the chaining. You get better status, reporting and efficient use of the system.