it all depends on money. I didn't have a lot when I picked up my bike...so my first upgrades were cheapo's...
- pedal cages/straps, minipump, gloves, tools + bag, and then later into bigger stuff...

for tools, I'd also recommend tire levers - but would actually steer clear of the hydro-pack for now...depending on money constraints...I've had ye ol' bottle rack for a long time, and if you're not going on extremely long treks a 50$ hydro-pak may be a bit much - I've survived alright...just make sure you drink. anyways...make sure you get all the oil/lube/degreaser/brushes etc. so you can fully clean and lube the bike...because that will make a world of difference.
another thing is a book...a good bike repair book...it'll help you get a better idea of the guts of the bike, and you can get an idea of future upgrades you might want...
anyways...take care of necessities before cosmetics...and think practical...if you're gonna commute with the bike, it might not be wise to put on clipless petals which require dedicated shoes...especially if you don't want to bring a backpack with you wherever you go with a change of shoes...
anyways...enjoy...upgrading's the funnest part, other than riding that is...
Timothy.