As the immortal bard once said:
"To crush or not to crush,
that is the question.
Whether tis nobler to crush the clove thus increasing its antifungal properties,
or to eat it whole ..."

Well now we can answer that question with the help of modern science.
http://www.garlic-central.com/allicin-chemistry.html

The major medicinal compound obtained from garlic is allicin, a powerful anti-biotic and anti-fungal. Allicin does not occur in garlic naturally. Instead, garlic cloves contain the amino acid alliin (S-allylcysteine sulphoxide):



When garlic is crushed or otherwise damaged, the alliin reacts with the enzyme allinase, also found naturally in garlic. Allinase acts as a catalyst and results in the transformation of alliin into allicin (diallyl thiosulphinate):



So if you want to use garlic as an antifungal, eat it raw and eat it crushed.

Another related point is whether garlic hurts good bacteria or not:
http://www.townsendletter.com/July2004/unseenepidemic0704.htm

The antimicrobials allicin from garlic, cinnamaldehydes from cinnamon, and also berberine from goldenseal have been found to profoundly inhibit overgrowth organisms such as Staphylococci, Coliforms, and yeasts without affecting Lactobacilli and Bifidobacteria (Rees et al., 1993). The inhibitory effects of allicin against Salmonella, Staphylococcus aureus and E. coli are visually depicted:



Table 1. MIC(minimum inhibitory concentration) of allicin against various microorganisms