>temp

      Var1                Freq1
1   file-upload             1
2   image-processing        1
3     mime-types            1
4       php                 5


>top

        Var2               Freq2
1   file-upload             1
2   image-processing        1
3     mime-types            1
4       php                 5
5      upload               1
6      firefox              2
7   machine-learning        1
8     matlab                1
9        r                  2
10      c#                  7

m1 <- merge(temp, top, by.x = "Var1", by.y = "Var2", all.x = TRUE)

Var1               Freq1        Freq2
1   file-upload             1            1
2   image-processing        1            1
3     mime-types            1            1
4       php                 5            5

x <- split(m1, m1$Var1)

$c#
[1] Var1 Freq1  Freq2
<0 rows> (or 0-length row.names)

m1$Var1 <- factor(m1$Var1)

x <- data.frame(var=letters[1:3],freq1=1:3)
y <- data.frame(var=letters[2:4],freq2=2:4)

merge(x,y)$var
[1] b c
Levels: a b c

droplevels(merge(x,y))$var
[1] b c
Levels: b c