You want the (standard) POSIXt type from base R that can be had in 'compact form' as a POSIXct (which is essentially a double representing fractional seconds since the epoch) or as long form in POSIXlt (which contains sub-elements). The cool thing is that arithmetic etc are defined on this -- see help(DateTimeClasses)
Quick example:
R> now <- Sys.time()
R> now
[1] "2009-12-25 18:39:11 CST"
R> as.numeric(now)
[1] 1.262e+09
R> now + 10 # adds 10 seconds
[1] "2009-12-25 18:39:21 CST"
R> as.POSIXlt(now)
[1] "2009-12-25 18:39:11 CST"
R> str(as.POSIXlt(now))
POSIXlt[1:9], format: "2009-12-25 18:39:11"
R> unclass(as.POSIXlt(now))
$sec
[1] 11.79
$min
[1] 39
$hour
[1] 18
$mday
[1] 25
$mon
[1] 11
$year
[1] 109
$wday
[1] 5
$yday
[1] 358
$isdst
[1] 0
attr(,"tzone")
[1] "America/Chicago" "CST" "CDT"
R>
As for reading them in, see help(strptime)
As for difference, easy too:
R> Jan1 <- strptime("2009-01-01 00:00:00", "%Y-%m-%d %H:%M:%S")
R> difftime(now, Jan1, unit="week")
Time difference of 51.25 weeks
R>
Lastly, the zoo package is an extremely versatile and well-documented container for matrix with associated date/time indices.