Theo was a great one, for sure, but he started getting away from focusing on the farm as a top priority towards the end of his time with Boston (same with the Cubs).
While he did draft Mookie his last year here (along with a few others- see below) , these were the top prospects he left for Ben, according to soxprospects.com:
1. Middy
2. Kalish
3. Ranaudo
4. Bogey
5. Iggy
6. Lava
7. Barnes
8. Brentz
9. Jacobs
10. Swihart
11. Coyle
12. Cecchini
13. Weiland
14. Doubront
15. A Wilson
16. D Britton
17. Vitek
18. Head
19. Pimental
20. Tejada
His drafts after 2005, despite having several comp picks didn't really measure up to the ones in 2003 and 2005.
Top 50 picks:
2006: Jason Place, Daniel Bard, Kris Johnson, Caleb Clay
2007: Nick Hagadone
2008: Casey Kelly, Bryan Price
2009: Reymond Price
2010: Kolbrin Vitek, Bryce Brentz, A Ranaudo
2011: Barnes, Swihart, Owens, JBJ (Betts with the 172nd pick)
The area he never seemed to let up in was international FA signings:
2004: Doubront
2006: Dice-K, Okajima
2008: Tazawa
2009: Bogaerts, Iglesias, Montas
2011: Margot
Ben got us Devers, DHern & Moncada that way.