Pouchitis
Ciprofloxacin is preferable to metronidazole1, because treatment with ciprofloxacin eradicates both pathogens (Clostridium perfringens and E. coli ) and results in an optimal restoration of normal pouch flora. Also, ciprofloxacin is better tolerated than metronidazole2.

Metronidazole (Flagyl) vs. Albendazole

Giardiasis
Albendazole and metronidazole are equally effective in the treatment of giardiasis3-4. Albendazole is better tolerated than metronidazole.

Metronidazole (Flagyl) vs. Vancomycin

Clostridium difficile-associated diarrhea
Metronidazole and vancomycin are equally effective for the treatment of mild Clostridium difficile-associated diarrhea (CDAD), but vancomycin is superior for treating severe CDAD5.

Further reading

References

1. Gosselink MP, Schouten WR, van Lieshout LM, Hop WC, Laman JD, Ruseler-van Embden JG. Eradication of pathogenic bacteria and restoration of normal pouch flora: comparison of metronidazole and ciprofloxacin in the treatment of pouchitis. Dis Colon Rectum. 2004 Sep;47(9):1519-25. Epub 2004 Jul 8. PubMed
2. Shen B, Achkar JP, Lashner BA, Ormsby AH, Remzi FH, Brzezinski A, Bevins CL, Bambrick ML, Seidner DL, Fazio VW. A randomized clinical trial of ciprofloxacin and metronidazole to treat acute pouchitis. Inflamm Bowel Dis. 2001 Nov;7(4):301-5. PubMed
3. Romero-Cabello R, Robert L, Munoz-Garci'a R, Tanaka J. Randomized study comparing the safety and efficacy of albendazole and metronidazole in the treatment of giardiasis in children. Rev Latinoam Microbiol. 1995 Oct-Dec;37(4):315-23. PubMed
4. Misra PK, Kumar A, Agarwal V, Jagota SC. A comparative clinical trial of albendazole versus metronidazole in giardiasis. Indian Pediatr. 1995 Mar;32(3):291-4. PubMed
5. Zar FA, Bakkanagari SR, Moorthi KM, Davis MB. A comparison of vancomycin and metronidazole for the treatment of Clostridium difficile-associated diarrhea, stratified by disease severity. Clin Infect Dis. 2007 Aug 1;45(3):302-7. Epub 2007 Jun 19. PubMed