Hey there, i'm coming over in September for a couple of weeks and wondering what and where is recommended to do/visit/stay. I will be traveling by public transport so am slightly limiting myself to destinations so i don't spend most of the two weeks on a bus. I'd love to here where you enjoyed and your stories as i've never been to Israel before and want to make the most of it. Cheers, Lizzie..
What are your interests? What do you want to see? Scenery, religious sites (any religion), history, hiking, beaches, restaurants, museums...
One thing you should bear in mind is the Jewish religious holidays that fall in September, which will disrupt your travel plans to no small extent, if you will be in Israel in the second half of the month. Rosh Hashana (New Year) starts on the evening of Friday September 18 and continues till after dark on Sunday September 20. There will be no public transport - buses or trains - in Jewish areas during this time. Shops and offices will be closed, but you might find taxis. Tourist sites will be open but probably very crowded.
Yom Kippur falls on September 28. From about 1 p.m. on Sunday September 27 transport will start winding down, coming to a complete halt by about 3 p.m. It will not resume until around 8 p.m. on Monday September 28. During this time everything in Jewish areas of Israel will be closed, including all shops, museums and tourist sites. There will be no taxis either. If you are in Israel then, unless you specifically want to experience Yom Kippur in Israel (I have no idea whether you are Jewish), my advice is to go to east (Arab) Jerusalem where everything will be open.
In addition, there is no public transport on Shabbat throughout the year - in September this means from about 5 p.m. Friday till about 8 p.m. Saturday.

Cheers for the tips, i'm actually just going the first half of the month though. I'm just after peoples highlights and what the enjoy/ enjoyed most about being in Israel. Thanks..

everyone has their own list of "must see" places in israel...
definitely spend a good chunk of time in jerusalem.
check out the free tour in the old city run by this company called sandemans new europe at 11 & 2:30 every day:
http://www.newjerusalemtours.com/index.php?option=com_content&task=view&id=12&Itemid=26
try to get reservation for the kotel tunnel tour:
http://english.thekotel.org/VisitorInfo.asp?id=1
try and spend a day at yad vashem, the holocause memorial museum:
http://www1.yadvashem.org/yv/en/visiting/index.asp
spend a couple days in tel aviv, some time relaxing on the beach, checking out the bar sign, just soaking up the "culture" there.
hike up masada for sunrise (or take the cable car if you're there later in the day) & float in the dead sea
spend a couple days in the galilee...check out the sea of galilee, the mystical city of safed, if you enjoy hiking there are some amazing hikes in this area...
that's a little bit to get you started, but everyone obviously has there own list of "must see" places...