URL Conditional in JavaScript
From a once over:


oneRoot and twoRoot are only needed in their respective if block, you should move the var statements to those if blocks.
This:

if(twodigit == 10) {
    lastURL = twoRoot + "9/";
    nextURL = twoRoot + "11/";
} else {
    lastURL = twoRoot + (twodigit - 1) + "/";
    nextURL = twoRoot + (twodigit + 1) + "/";
}


could simply be

    lastURL = twoRoot + (twodigit - 1) + "/";
    nextURL = twoRoot + (twodigit + 1) + "/";


I am not sure why you needed to call out the (twodigit == 10 case
urlData &lt;- Not sure what this does at all
var oneslash = currentURL.substr(currentURL.length - 2); &lt;- You are not using this
onedigit = oneslash.substr(0,1)*1; &lt;- You already captured this in lastChar, you could simply do onedigit = +lastChar;
You have 0 comments..
You did not declare onedigit with var
You have some indentation trouble towards the end of your code.


I have something like this: ( also on http://jsfiddle.net/konijn_gmail_com/unQQ7/ )

function linkSet() {
    var currentURL = location.href;
    var lastURL = "";
    var nextURL = "";
    var lastChar = currentURL.charAt(currentURL.length - 2);
    var secondLastChar = currentURL.charAt(currentURL.length - 3);

    if(isNaN(lastChar) === true) {
        //Hide left button, hard code right button to go to ../2
        var leftContain = document.getElementById('leftcontainer');
        var rightContain = document.getElementById('rightcontainer');
        leftContain.style.display = "none";
        rightContain.style.width = "100%";
        rightContain.style.float = "none";
        lastURL = currentURL;
        nextURL = currentURL + "2/";
    } else if(isNaN(secondLastChar) === false) {
        //The page number is a double digit, simply derive last/next
        var twoRoot = currentURL.slice(0, -3);
        var twoSlash = currentURL.substr(currentURL.length - 3);
        var twoDigit = twoSlash.substr(0, 2) * 1;
        lastURL = twoRoot + (twoDigit - 1) + "/";
        nextURL = twoRoot + (twoDigit + 1) + "/";
   } else {
       //The page number is single digit, with a special case for page 2
        var oneRoot = currentURL.slice(0, -2);
        var oneDigit = +lastChar;
        if(onedigit == 2) {
            lastURL = oneRoot;
            nextURL = oneRoot + "3/";
        } else {
            lastURL = oneRoot + (oneDigit - 1) + "/";
            nextURL = oneRoot + (oneDigit + 1) + "/";
        }
    }
    document.getElementById("lastlink").href = lastURL;
    document.getElementById("nextlink").href = nextURL;
}


If I had to write the code for a personal project, I would not distinguish between 1 char and 2 chars ( what if there are over a thousands pages ? ), I would just get the number from the URL and build the buttons from that. The code in that case would be easier to follow as well (to me at least). ( http://jsfiddle.net/konijn_gmail_com/xNQ7m/ )

function hideLeftButton() {
    var leftContain = document.getElementById('leftcontainer');
    var rightContain = document.getElementById('rightcontainer');
    leftContain.style.display = 'none';
    rightContain.style.width = '100%';
    rightContain.style.float = 'none';
}

function linkSet() {
    var currentURL = location.href,
        parts = currentURL.split('/'),
        lastURL, nextURL;

    //Get rid of "" ( because URL ends with / )
    parts.pop();          
    //Next part of the URL is the number ( or not )
    number = parts.pop();    
    //Build up the root to append numbers to
    var root = parts.join('/') + '/';

    if (isNaN(number) === true) { 
        hideLeftButton()
        lastURL = currentURL;
        nextURL = currentURL + '2/';
    } else if (number == 2) {
        lastURL = root;
        nextURL = root + '3/';
    } else {
        lastURL = root + (+number - 1) + '/';
        nextURL = root + (+number + 1) + '/';
    }
    document.getElementById('lastlink').href = lastURL;
    document.getElementById('nextlink').href = nextURL;
}