This isn't related to your question, but you want to use = and not <- within the function call. If you use <-, you'll end up creating variables y1 and y2 in whatever environment you're working in:

d1 <- data.frame(y1 <- c(1, 2, 3), y2 <- c(4, 5, 6))
y1
# [1] 1 2 3
y2
# [1] 4 5 6

This won't have the seemingly desired effect of creating column names in the data frame:

d1
#   y1....c.1..2..3. y2....c.4..5..6.
# 1                1                4
# 2                2                5
# 3                3                6

The = operator, on the other hand, will associate your vectors with arguments to data.frame.

As for your question, making a list of data frames is easy:

d1 <- data.frame(y1 = c(1, 2, 3), y2 = c(4, 5, 6))
d2 <- data.frame(y1 = c(3, 2, 1), y2 = c(6, 5, 4))
my.list <- list(d1, d2)

You access the data frames just like you would access any other list element:

my.list[[1]]
#   y1 y2
# 1  1  4
# 2  2  5
# 3  3  6