From what I have read it seems like while the brothers were alive they did cause a lot of changes in the political system of Rome but once they were both killed by the Senate it seems like in large part their reforms were overturned or ignored. So what was their actual long term effect to the Roman system if they had one?
Do you have examples of Gracchan actions that were overturned or ignored? Because I can't think of any. By "reforms"--a terribly anachronistic concept, since the Romans had no constitutional government to reform--I assume you mean the various leges Semproniae passed by Gaius and Tiberius Gracchus. Running down the list:
Tiberius' agrarian law was revived by Gaius, and though alternate agrarian proposals by the tribune Livius Drusus were also floated the Gracchan agrarian laws appear to have been basically upheld by the lex agraria of 111, which converts various types of land into public land. The exception to the general acceptance of the actions of the Gracchan land commission is C. Gracchus' colony at Carthage, which had already failed by the time of the lex agraria of 111. Related to this is Tiberius Gracchus' decision to bring to plebiscite the question of the division of Attalus' property, which by normal custom was the right of the senate. Stockton's argument that this, along with his decision to run again for the tribunate, is what got Ti. killed is, to my knowledge, generally accepted, but the decision reached by the plebiscite held. C. Gracchus' law establishing the sale by the censors of the Asian tribute became the basis for tributary collection in Asia until the end of the Republic
C. Gracchus' lex de judicaria was upheld for about forty years. For a little while at the beginning of the first century juries for repetundae trials were transferred back and forth between the senate and equites, but the lex Valeria of 70 established firmly and clearly that these juries were to be divided between senators and equites.
C. Gracchus' lex de provinciis consularibus became the basis for provincial administration in the late Republic, and an especially important component of elections after Sulla established that the consuls would not depart for their consular provinces until after the end of the year. Importantly, the lex de provinciis consularibus established that the distribution of consular provinces was immune to tribunician veto.
C. Gracchus' lex de frumentaria established state-subsidized grain to the measure of 5 modii per month. In 58 this was distributed gratis by the lex Clodia, although by late 57 Pompey's cura annonae, formed in response to some sort of shortage (real or more likely artificial), had imposed limits on the eligibility of the state-subsidized grain, and under Caesar and Augustus its scope was severely limited. Nonetheless, hardly a law that was overturned or ignored--the lex frumentaria was expanded by later tribunes.
C. Gracchus' lex de capite civium remained in force throughout the existence of the Roman state. It was the basis for Cicero's exile in 58, since he had executed the Catilinarians without trial
C. Gracchus' legislation in support of public works and the terms of military service are hard to track down, but appear uncontested
C. Gracchus' agitation in favor of the Italians is a complicated subject made no easier by the confusion of the sources. His measures appear not to have gone through, but the result of the Social War was Italian enfranchisement, and support for Italian citizenship appears periodically throughout the late second and early first centuries, leading up to the Social War.
To this we should add two of Ti. Gracchus' actions, both of which became established precedent. In the first place, Ti. Gracchus overrode his colleague Octavius' veto, and went so far as to call a vote of the assembly to abrogate Octavius' magistracy. This vote was successful, and Octavius was stripped of his tribunician powers. The precedent established by Ti. was so prevalent that since Mommsen there has been great debate over whether Ti. in 133 weakened the tribunician veto or not. Certainly Gracchus--or more accurately, Octavius--introduced new procedures to the legislative veto, in that Octavius vetoed for the first time the actual reading of a bill, which became accepted practice thereafter, prompting an amusing attempt by Cornelius in 67 to begin reciting his vetoed bill by memory, since he could not physically read it. Nonetheless, not only was it uncontested, but it was even defended by those whom we might expect to be most opposed to the Gracchi's actions. In defending Gabinius' decision as tribune in 67 to call on the assembly to vote to abrogate his colleague Tribellius' magistracy when Tribellius vetoed his legislation, Cicero remarked that neque...passus est plus unius collegae sui quam universae civitatis vocem valere et voluntatem, "Nor did he permit the voice and will of one of his colleagues to be stronger than the voice and will of the entire people." This is extremely close to what Plutarch claims Ti.'s reasoning was, namely that a tribune is sworn to uphold the rights of the people, foremost of which is the citizen assemblies: if a tribune prevents the assemblies from functioning, he has surrendered his position as tribune already. Additionally, the precedent set by Ti. Gracchus that the tribunate could be sought out again was generally accepted in the decades following. Ti. was killed before the elections were completed, but C. held the tribunate twice, and Saturninus a couple decades later did as well.
Even the method of C. Gracchus' demise was formally accepted into Republican practice. Though Ti. was killed with no official support, C. was killed as the result of what modern scholars call a senatus consultum ultimum, which was passed for the first time to allow Opimius the powers to use military force against Gracchus within the city. Modern readers scratch their heads over the SCU a lot: it had no legal backing, and contained no clear rules, guidelines, or limitations. Yet the right of the senate in times of crisis to call on the consuls to act to protect the state was universally accepted--not even Caesar disputes the legal validity of the SCU called against him.