Contributions to social security (including pension and healthcare) will be automatically deducted from your salary. You contract states your gross salary before any deductions. This is if your job is an actual full-time position (i.e. with a monthly salary, not some sort of freelance position). Note that that these deductions are quite substantial, so if you do not know how this works you should really get up to speed before you sign anything (else you won't know how much money you have actually available per month).

Holiday allowance ("Urlaubsgeld") is a matter of negotiations (but while it was once customary it's for the most part an obscure thing of the past now). It's certainly not usual in IT position.

"Weihnachtsgeld" (some extra money on your December salary) is a little more usual. However in IT this is usually not a part of the contract, rather the companies pay this on a "voluntary" basis (meaning they can choose not to pay it at all, e.g. if the business year wasn't that good).

Another thing to discuss would be "variable Gehaltsbestandteile" - bonuses, basically. However bonuses are more usual for sales people and managers, not so much for engineers. 

One thing to keep in mind is that the tax system is progressive, so you will pay a disproportionate amount of taxes on bonuses. That's why many people prefer a somewhat higher base salary over bonuses (even if at face value the bonus would pay more).

Travel expenses are usually handled on a case by case basis, but you should ask during job negotiations if there is a budget for travel and on which basis this is allocated.